01[11] <java> i guess we'll start discussing the lecture
[11] <mchia> Maybe some of them are in the chemistry channel.
01[11] <java> lol - like the first day? or is it scheduled for the same time?
[11] <walla2butterfly> maybe thought they were doing wes
[11] <walla2butterfly> yes
01[11] <java> that chat is the same time?
[11] <walla2butterfly> but you answered that question on the forum, so they should no
[11] <walla2butterfly> read that chem was doing chat on wes evenings
01[11] <java> oh, got worried
[11] <walla2butterfly> wrong "no" Know
[11] <mchia> It's from 10 to 12 EST
01[11] <java> ah
01[11] <java> thanks mchia
[11] <mchia> I'm also on it now
[11] <walla2butterfly> do you like it is it worth it
[11] <mchia> the chemistry channel
01[11] <java> are there people there?
[11] <mchia> 6 including me & instructor
03[11] * Rob ([email protected]) has joined #micro08
01[11] <java> wow - and it's not even scheduled time an people are there in that chat channel??
[11] <walla2butterfly> hi Rob
01[11] <java> hi rob
[11] <Rob> hi, I'm actually trying to balance to channels
01[11] <java> are you in chem as well?
[11] <walla2butterfly> tell them to get their but... to class
[11] <Rob> yes
01[11] <java> wait - so is chemistry chat scheduled for today or wed? is that chat right now impromptu or scheduled?
[11] <walla2butterfly> I wasnt sure whether it was worth another 75 bucks, and I have looked at the material seems kind of elementry,
[11] <mchia> It's scheduled.
[11] <mchia> They changed it to today
01[11] <java> ok, i guess that explains the low turnout
[11] <mchia> Wade said students can use two windows for both channels
[11] <Rob> The chat gets deeper then the reading material
[11] <walla2butterfly> was wondering about that
[11] <walla2butterfly> maybe I will join then
[11] <walla2butterfly> maybe get a clearnce deal seeing how it is half over
01[11] <java> well i guess we'll start anyhow
[11] <walla2butterfly> k
01[11] <java> start talking about microbial habitats and their considerations
01[11] <java> which will logically lead to manipulation for our tanks
[11] <mchia> OK
01[11] <java> some basic considerations are 1) oxygen levels
01[11] <java> because obviously control of these leads to control of various steps of the nitrogen cycle
01[11] <java> for example, proving anaerobic microenvironments can help facilitate denitrification
01[11] <java> another which is still a consideration, but somewhat limited in a reef aquarium
01[11] <java> is temperature
Session Close: Sat Jan 26 11:27:40 2008
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03[11] * Now talking in #micro08
03[11] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[11] * Set by wade on Wed Dec 31 19:00:01
01[11] <java11> wow sorry
01[11] <java11> not sure what happened
01[11] <java11> got kicked off and a big text box about usage rules
01[11] <java11> anyhow
[11] <walla2butterfly> mmm still listed though
01[11] <java11> hm
01[11] <java11> and this wass the altername nick i provided
01[11] <java11> i'm just going to keep talking on this so as not to waste any time
[11] <walla2butterfly> so limited in a reef
01[11] <java11> we can't do THAT much about temp
01[11] <java11> in a reef, because the limits are very narrow
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03[11] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[11] * Set by wade on Wed Dec 31 19:00:01
01[11] <java> so for example
01[11] <java> say you normally keep things at low 80s
01[11] <java> and you get a death
01[11] <java> and a resulting cyanobacterial bloom
01[11] <java> lowering temp by a few degrees over a couple days could actually make a difference in growth rates
01[11] <java> so that any predators you might have, snails, etc
01[11] <java> could catch up
01[11] <java> other factors in miccrobial habitats are pH
01[11] <java> which isn't manipulated by the aquarist
01[11] <java> but rather by the bacteria themselves to create microenvironments
01[11] <java> and light penetration
01[11] <java> one topic i wanted to get into greater detail with
01[11] <java> is the idea of a concentration gradient
01[11] <java> which isn't in the lecture
01[11] <java> by now we've all realized the idea that there are "anaerobic" and "aerobic" zones
01[11] <java> to use a relevant example
02[11] * java11 ([email protected]) Quit (Ping timeout)
01[11] <java> however, there is rarely a definite line betweent he two zones
01[11] <java> espescially when we start looking at the scale of bacteria , and on a molecular level
01[11] <java> in one of the papers for today
01[11] <java> they get into this idea
01[11] <java> that although on a macroscopic level one might be able to take a O2 sensor
01[11] <java> put it into sand at varying depths
01[11] <java> and determine that there is a delineation at a certain depth in the sand between oxic and anoxic environments
01[11] <java> measure it at "10mm" and call it a day
01[11] <java> if you were to zoom in one the millimeters above and below this "line"
01[11] <java> you'd find, at some scale, a slow lowering of oxygen, along a concentration gradient, as you go down
01[11] <java> at 8 mm you might see half of wht you see at the surface
01[11] <java> at 9mm perhaps 1/4th
01[11] <java> and then at 10mm perhaps not exactly zero, but 1-10%, but lower than the threshold for the probe
01[11] <java> so realize that at some scale there is rarely a definite "line" between 100% and 0% concentration
01[11] <java> always a gradient, a range where the measurement of whatever variable you are interested in becomes lower as the experimental variable changes
01[11] <java> in this case, depth measurement
01[11] <java> so, why do we care?
01[11] <java> well
01[11] <java> because in the case of dissolved oxygen
01[11] <java> and the facilitation of anaerobic microenvironments
01[11] <java> there is a direct application for reefkeeping
01[11] <java> in terms of facilitating denitrification
01[11] <java> because dissolved oxygen is a direct result of things like water agitation and flow
01[11] <java> in a high flow tank, that measured threshold of around 10mm at one flow point
01[11] <java> might be doubled with the higher flow
01[11] <java> if it is high enough
01[11] <java> similarly, one must consider these microhabitats during setup in terms of sand and rock
01[11] <java> using an extreme case
01[11] <java> a bare-bottom tank, with little rock, but high bioload
01[11] <java> and high flow, might have a problem with nitrates
01[11] <java> resulting from the sparsity of anaerobic niches
01[11] <java> at the extreme other end
01[11] <java> a low bioload, low flow tank with a substantial sandbed and a lot of rock
01[11] <java> would likely never have any measurable nitrates in the water column
01[11] <java> by low bioload, that also means free of detritus
01[11] <java> so depending on one's preferences and goals
01[11] <java> these variable should be considered and manipulated accordingly
01[11] <java> variables
01[11] <java> any questions?
01[11] <java> another variable along these lines of manipulating oxygen content in microbial habitats
01[11] <java> is the substrate itself
01[11] <java> obviously the ability if water to diffuse between the sandbed substrate plays a role
01[11] <java> something like crushed coral for example, with a vary large particle size
01[11] <java> might be aerobic down a couple inches
01[11] <java> and the fact that it contains large spaces might become problematic when trapping detritus
01[11] <java> in this case, any denitrification capacity would be accompllished by any live rock in the system and iside each particle of crushed coral
[11] <mchia> So is substrate size is a way to control oxygen in the substrate?
01[11] <java> yes
[11] <mchia> Thanks.
01[11] <java> np - conversely
01[11] <java> a very fine substrate size has it's own set of considerations
01[11] <java> obviously the particles will fit together much more snugly
01[11] <java> impeding flow of oxygenated water downwards
[11] <walla2butterfly> less o2, more anaerobic guys
01[11] <java> yes
01[11] <java> however, ideally one should strike a balance
[11] <walla2butterfly> does this help in the cycling ?
01[11] <java> during the initial cycle things are sorting out
[11] <walla2butterfly> k
01[11] <java> but the consideratioin i'm discussing
01[11] <java> comes more into play in terms of planning out a long term habitat for bacteria
01[12] <java> considerations
01[12] <java> so when we switch to a really fine substrate
01[12] <java> something else needs to be considered
01[12] <java> which is the formation of biofilms
01[12] <java> bacteria in environment
01[12] <java> frequently facilitate their own space to some degree
01[12] <java> by this i mean that they can sort of "build their own house"
01[12] <java> and lilve in communitites
01[12] <java> live
01[12] <java> in the lecture presentation
01[12] <java> there was an illustration of formation and structure of biofilms
01[12] <java> bacteria in nature
01[12] <java> frequently are encapsulated
01[12] <java> this capsule whihc they form themselves
01[12] <java> are typically made up of sugars and proteins produced and secreted by the bacteria
[12] <walla2butterfly> which pg for the illustration
01[12] <java> page 8
[12] <walla2butterfly> ty
01[12] <java> in a way, bacteria make their own "clothes" so to speak, this capsule is something they "wear"
01[12] <java> and it serves a simialar function as clothing for humans
01[12] <java> it protects them from their environment
01[12] <java> and it also serves as a matrix by which they can influence the true microenvironment, right up against their "skin" or their cell wall
01[12] <java> many capsules have degradative enzymes which process environmentla substrates
01[12] <java> and there can be enzymes which help to keep a specific, fine-tuned pH nearby as well
01[12] <java> it's actually more like a space-suit than regular clothing
[12] <walla2butterfly> so make their own environment in a way??
01[12] <java> because it is "active"
01[12] <java> yes, to a certain degree
01[12] <java> but it's also limited by the true environment around them
[12] <walla2butterfly> right they probably can only control so much
01[12] <java> exactly
01[12] <java> so, enters the biofilm
01[12] <java> bioifilms are like little towns and cities, communities of bacteria
01[12] <java> where they stay together after multiplyng
01[12] <java> their capsules become spatially intertwined
01[12] <java> some bacteria dies, but their capsules and dead cells don't really physically leave, but get incorporated into the interstitial matrix between cells
[12] <walla2butterfly> (takes a village to raise a bacteria, LOL. sorry couldnt helpit)
01[12] <java> lol
01[12] <java> and when these things really become established, a film visible to the naked eye can form
01[12] <java> a biofilm
01[12] <java> it may just feel like a slimy coating
01[12] <java> but it's actually a bacterial community
01[12] <java> so getting back to what i was talking about regarding grain sizes
[12] <mchia> Once you can see it, does it become a microbial mat?
01[12] <java> yes, when these thigs grow undisturbed for a long time, they become microbial mats
[12] <walla2butterfly> what is the diff between the bioflim and mat
01[12] <java> the lower depths of microbial mats actually harden and become rocklike
[12] <walla2butterfly> k
01[12] <java> and true "mats" are really really old
01[12] <java> on the order of centuries/millenia
[12] <walla2butterfly> like how old?
[12] <walla2butterfly> okay
[12] <walla2butterfly> so we wouldnt have mats in our tanks
01[12] <java> it's the microbial version of a reef
01[12] <java> no
[12] <walla2butterfly> gotcha
01[12] <java> but it's like a reef in that the reef foundation is coral skeleton form thousand of years ago
01[12] <java> from thousands
[12] <walla2butterfly> okay grain size
01[12] <java> in a small grain size
01[12] <java> because of how tightly fitting the grains are
01[12] <java> microbial communities from neighboring grains can form intertwined biofilms more readily
01[12] <java> if you look at a typical oolite sandbed, against glass
01[12] <java> you can resolve visually the grains because there's visible space between them
01[12] <java> and bacterial communities will only intertwine with others they can physically touch
01[12] <java> but with a fine powdery sand
01[12] <java> the entire sandbed can become an intertwined bacterial community
01[12] <java> and along with the aragonite dissolution and subsequent precipitation that can cause sandbeds to "fuse" or harden
01[12] <java> then one can visualize where the majority of the sandbed might become dangerously immobile, and anoxic
[12] <walla2butterfly> ?
01[12] <java> the
01[12] <java> "gradient" i described earlier would be closer to the surface
[12] <walla2butterfly> so not to fine either
[12] <mchia> So if the sand bed fuses, it can be a bacterial problem?
01[12] <java> because biofilms are on inspection an actual physical goo
01[12] <java> which is thicker than water
[12] <walla2butterfly> so too much no water ( environment)
01[12] <java> then oxygen diffuses even more slowly than if what wass between the grains was jsut water
01[12] <java> right
01[12] <java> the dissolved oxygen not only may diffuse slower, but not at all, ever
01[12] <java> if there's an actual physical blockage composed of hardened sandgrains and think goo where there might normally be a little space for water
01[12] <java> thick
01[12] <java> it's all about middle ground
01[12] <java> you want to facilitate a biofilm
[12] <walla2butterfly> thinking stinking mud?
01[12] <java> but not one that gets so thick that water can't ever penetrate
01[12] <java> yep! it'll defintiely get stinky
01[12] <java> and don't forget what we covered in another chat
01[12] <java> that just because water can get through
01[12] <java> it does NOT mean that water is oxygenated
01[12] <java> because it gets consumed by bacteria as it circulates downwards, and this consumption depletes the water of oxygen rather quickly
01[12] <java> so the anoxic, anaerobic habitats aren't because water doesn't circulate
01[12] <java> but because it circulates slowly enought through the bed that it can get consumed
01[12] <java> so a really anaerobic bed isn't good if water (and thereby nutrients AND WASTE!!) can circulate
[12] <walla2butterfly> the oxygen?
01[12] <java> ah i see
01[12] <java> water circualted slowly enough through the bed that oxygen can get consumed
[12] <walla2butterfly> okay, on the upper level right
01[12] <java> yes, AND along a gradient, the O2 levels will decrease as depth increases
[12] <walla2butterfly> gotcha
01[12] <java> there's ALWAYS a gradient, unless it's somemthing completely imnpermeable like glass or plastic
01[12] <java> but in terms of the surface of live rock
01[12] <java> or a sandbed
[12] <walla2butterfly> right you dont starve to death over night
[12] <mchia> Hence are there also gradients of bacterial types?
01[12] <java> yes - very good
01[12] <java> the aerobic bacteria will find their happiest spots adn grow well there
01[12] <java> some of those same might adapt to different conditions, grow slower, be less populous, but still be ther as you go down
[12] <walla2butterfly> yes there are the ones that can use oxygen or not, and those who could careless if it is there
01[12] <java> right!
01[12] <java> you guys defintely are getting this
[12] <walla2butterfly>
01[12] <java> i think this is a good time for a 10 minute break
[12] <walla2butterfly> k
01[12] <java> but first, any other questions?
01[12] <java> ok, i'll be back by 12:47
[12] <walla2butterfly> or 9:47
[12] <walla2butterfly> so rob, are you out there
[12] <Rob> yes I'm here
[12] <walla2butterfly> so are you Bob? ( from last week)
[12] <Rob> Yes, the chat wouldn't let me sign on with the same name on two channels.
[12] <walla2butterfly> okay was wondering if it was the same, but I actually had a ? for you but for the life of me I cant remember what it was. Have to work on that
[12] <Rob> I've been out of town at business meeting so now I'm trying to catch up.
[12] <walla2butterfly> kind of interesting stuff , dont you think, or is stuff you already knew
[12] <Rob> It's stating to take the aquarium to a new level for me
[12] <walla2butterfly> I hear that stuff I never thought about before. Your in the chemistry also
[12] <Rob> The chemistry is good but it's still at the basic level. I'm hoping it evolves like this one.
[12] <walla2butterfly> think it is worth joining ( paying) at this point?
[12] <walla2butterfly> heard the lecture/chat is more involved
[12] <walla2butterfly> I have looked at the lit, seemed pretty elementry
[12] <Rob> As far as catching up no problem. The chats go into some good tank problem solving.
[12] <walla2butterfly> do they post the old chats?
[12] <Rob> At this time I would say chem=high school level & this one is definately=college.
[12] <Rob> Yes they do
[12] <walla2butterfly> have to think about it
[12] <walla2butterfly> harder that is
[12] <Rob> Mchia, you're in both. What do you think?
[12] <walla2butterfly> we were talking about it at the beginning before you joined, that is where I heard the chats were good
[12] <mchia> The other chat is more a discussion
[12] <Rob> agreed
[12] <mchia> This is more of a lecture
[12] <walla2butterfly> do they use the forum
[12] <mchia> Not really.
01[12] <java> that's what i'm curious about
[12] <walla2butterfly> I like the lecture breaks down the reading and sums it up
01[12] <java> i'm surprised more people don't use the forum
[12] <mchia> Maybe that's why it's more of a discussion
[12] <mchia> on the chemistry side
[12] <Rob> True I'm posting an issue today. Maybe it'll give more life to the forum.
01[12] <java> ah, thank you
01[12] <java> i said in one of the threads we need a TROLL!
01[12] <java> someone to get everyone riled up
[12] <walla2butterfly> so I am curious about the rock you were about to talk about
[12] <walla2butterfly>
01[12] <java> i was on another forum and someone posted about how you really SHOULD pee in your tank to cycle it and the topic exploded
[12] <walla2butterfly> obvious I am not a troll, dont have the hair for it
01[12] <java> no - a forum troll is someone who makes a post to get peoplpe annoyed
01[12] <java> people
[12] <Rob> I heard about that cycling method.
01[12] <java> yeah, it's out there
01[12] <java> oh right - the rock
01[12] <java> let's think for a scond what "live rock" really is
01[12] <java> second
01[12] <java> it's the old skeleton of dead coral
01[12] <java> and if you've ever taken a look at a freshly deceased coral skeleton
01[12] <java> you'd see that it's highly porous, highly structured
01[12] <java> as an animal skeleton, there are a lot of specialized structures
01[12] <java> nooks, holes, and the calcium carbonate is REALLY porous if you were to look at it under a dissecting scope
01[12] <java> this is basically the underlying structure of what we're dealing with
01[13] <java> once it
01[13] <java> it's dead,
01[13] <java> as in the rest of nature, the dead space quickly becomes filled with life
01[13] <java> at the level we're considering, it's a GREAT structure for biofilm formation, with the films covering the insides of pores, the surfaces of specialized skeletal structures, etc.
01[13] <java> obviously ther's other life to consider
01[13] <java> protists
01[13] <java> small animals like worms
01[13] <java> algaes, coraline and macro
01[13] <java> all colonize these surfaces
01[13] <java> if you've ver broken up live rock to make it fit in the aquarium
01[13] <java> you'll see tunnels from the larger worms
01[13] <java> and sometimes localized areas deep within of a black or rusty color
[13] <mchia> What kinds of worms?
01[13] <java> bristleworms, eunicids, fanworms, all dig into the rock
[13] <mchia> Tube worms or bristle worms?
01[13] <java> yep
[13] <mchia> OK
01[13] <java> eunicids actually tunnel in, adn can be quite long
01[13] <java> and
01[13] <java> and they live such a reclusive life that you may not even know they're there unless you crack open a rock
01[13] <java> suffice to say, live rock is very, very "alive"
[13] <walla2butterfly> eunicids= are they what they call "peanut worms"?
01[13] <java> i'm not sure about nicknames
[13] <walla2butterfly> k
01[13] <java> they're scary looking, have scrapers which can burrow through calcium carbonate, look like they'd take off a pinky
[13] <walla2butterfly> ugh
01[13] <java> on the really big ones
01[13] <java> i saw pics somewhere of someone who found one 3 feet long in a not huge system
01[13] <java> can't remember how big
[13] <walla2butterfly> WOW
01[13] <java> yeah, when he found it he said he nearly peed his pants lol
[13] <walla2butterfly> "girlie"face and chills (here)
01[13] <java> lol
[13] <mchia> I think they are called bobbit worms
[13] <Rob> peanut worms are sipunculids
[13] <walla2butterfly> ty
01[13] <java> thanks!
01[13] <java> anyhow, all these organisms play a role
01[13] <java> and the structures i've mentioned play a role as well
[13] <walla2butterfly> never thought about a bigger tank for my worms ( think he will buy into it)
01[13] <java> coral skeletons near the surface of rock is very porous
01[13] <java> and these pores function in a manner analogous to the spaces of between grain of sand which we've already discussed
01[13] <java> so it's possible to form a gradient of oxygen between the surface and deeper down
01[13] <java> as well as provide a nice physical sructure for biofilm formation
01[13] <java> but with the rock, because the type/quantity of life is greater than sand
01[13] <java> biofilm thickening and hardening is less likely
01[13] <java> because physical niches may be occupied by other organisms
01[13] <java> whereas the sand bed really is the domain for bacteria
01[13] <java> but you also have to picture the physical substrate a little differently than a sandbed
01[13] <java> when considering gradients
01[13] <java> a sandbed is fairly uniform at it's surface, flat
01[13] <java> the gradient follows the contours of the sand as it rises and falls
01[13] <java> because the depletion of oxygen under conditions of O2 levels and flow are fairly constant, if the sand is uniform across the tank
01[13] <java> similarly, these O2 gradients in live rock will also follow the contours of the rock, across all nooks and crannies, but also IN THE TUNNELS
01[13] <java> oxygenated water will be able to enter the rock itself via some of the tunnels
01[13] <java> sometimes going quite deep
01[13] <java> or completely through
[13] <Rob> So the live rock has a large surface area
01[13] <java> however, this doesn't mean that the entire inside of the rock is oxygenated
01[13] <java> Rob - yes
01[13] <java> but the gradient will vary depending on the O2 levels in water traveling through the pores
01[13] <java> and tunnels
01[13] <java> now considering that most rock *probably* isn't as penetrable as a sandbed
[13] <walla2butterfly> lower on the rock closer to the sand would be less O2?
01[13] <java> if it were actually sitting on the sand then yes, at the area actually restricted from flow
[13] <walla2butterfly> k
01[13] <java> *probably*, because there is a great variety out there of rock and sand
[13] <mchia> How about if the rock was partially buried?
01[13] <java> there's lace rock, and seeded terrestrial rock like from Tampa Bay Saltwater
01[13] <java> lace rock being so porous that it might not actually support any anaerobic niches at all
01[13] <java> and the hard, non-porous seeded terrestrial rock isn't porous because it isn't made up of structured coral skeleton, but solid rock crystals
[13] <walla2butterfly> interesting
01[13] <java> so those are the extremes, and people actually use a lot of different thinngs for their LR, or somemtimes "base rock"
[13] <walla2butterfly> about the seeded rock
01[13] <java> all have varying capacities for life and for supporting denitrification
01[13] <java> oh, the seeded rock
[13] <walla2butterfly> well its all interesting
01[13] <java> yeah, so harvesting of carribean/florida reefs is prohibited
01[13] <java> so TBS dumps rock into the oceam, lets it sit for a few years during which it gets colonized
[13] <walla2butterfly> have read that and they claim it is the same but obviously not
01[13] <java> I've seent their rock and it's VERY ful of life - at the surface
01[13] <java> full
01[13] <java> very pretty stuff
01[13] <java> but although i've never used it, i suspect it can't be very good for biological filtration
01[13] <java> as live rock is typically used for
01[13] <java> so again, these considerations are important for setup
01[13] <java> when you're thinking about what you want to keep
01[13] <java> and designing a habitat to support it, biologically
[13] <walla2butterfly> and being as natural in bio as possible
01[13] <java> yeah - i'm a big proponent of a really deeply thought out system on the biological end
01[13] <java> and just letting it do it's own thing
01[13] <java> set it up, do water changes and prune
01[13] <java> but not much else
01[13] <java> because really, the less you futz with a tank, the happier the inhabitants, i.e. corals seem to be
01[13] <java> I set up my tank in September
[13] <walla2butterfly> some say you should change out some LR every now and then?
01[13] <java> well... i think that depends
01[13] <java> botgh on how things hahve been going and timeframe
01[13] <java> both
[13] <walla2butterfly> they say to reguvinate the tank
01[13] <java> well, here's the thing
01[13] <java> one reason i like the soft cycle is because it preserves the original diversity as much as possible
01[13] <java> on a reef things are really competitive for space
01[13] <java> BUT
01[13] <java> a lot of people who use the traditional method for cycling and curing rock
01[13] <java> well, curing, really
01[13] <java> of sticking it in a bucket, letting things die and rot, the "bucket of death" lol
01[13] <java> kills off SO much life
[13] <walla2butterfly> you end up with an uneven balance?
01[13] <java> and what you end up with is a micro-ecosystem out of balance once things recover
01[13] <java> HAHA veryy good
01[13] <java> yeah, and when things grow back, the competition is gone
[13] <walla2butterfly> TY, so in sept, your tank
01[13] <java> things become predominant that shouldn't be
01[13] <java> oh, right, i was saying that after the first 2 weeks, my hands have been in my tank maybe 3 times, and i haven't moved a frag or rock AT ALL
01[13] <java> because i think that corals grow best when they aren't disturbed
01[13] <java> they're not used to being moved around
01[13] <java> they sit in one place and grow foe 300 years
01[13] <java> for
[13] <Rob> With an existing tank, can you softcycle LR in a seperate tank and then add it to the main tank when the levels drop?
01[13] <java> yeah, i think that would be a great way to make it more practiccal
01[13] <java> the reason i brought up my tank wass just to illustrate that i like to think about setup and placement, set it up, then jsut not mess with it
01[13] <java> at all
[13] <walla2butterfly> always QT my LR,so I guess in a way I do soft cycle them
01[13] <java> as long as you don't let ammonia spike it would still be tecjhnically a "soft cycle"
01[13] <java> one other note
01[13] <java> people think that you *NEED* that ammonia spike to "get things going"
01[13] <java> not true
01[13] <java> the nitrogen cycle is ubiquitous - it's going on all around us, all the time
01[13] <java> in oceans, ponds, lakes
01[13] <java> BUT ALSO
01[13] <java> in the soil in your yard, even in a crack between the sidewalk
01[13] <java> everywhere
01[13] <java> what this means is that the nitrogen cycle is "unbreakable"
01[13] <java> things just always balance out
01[13] <java> it's can't not balance out, it's the natural order of things
01[13] <java> and additionally, you don't need to add any external sources of ammonia to get ammonia in a new system
[13] <walla2butterfly> ?
01[13] <java> because ammonia comes from the breakdown of all living materal
01[13] <java> if your'e adding live rock, there's going to be detritus on it
[13] <walla2butterfly> so if you put "dead" sand in a tank it would still produce some ammonia
01[13] <java> it's going to come with things like pods and worms, and there is always going to be a certain amount that dies off from the trip from the reef to your tank
[13] <walla2butterfly> and would it produce the right kind of bacteria
[13] <mchia> What if you sterilize it?
01[13] <java> it produced food for the bacteria, in the form of ammonia
01[13] <java> if you were to buy live rock and sterilize it, you'd kill everything and would have a lot of dead matter
01[13] <java> you'd get a massive ammonia spike
[13] <walla2butterfly> what if it was a large tank ( lots of water) and small rock, would you be okay with the ammonia and then slowly add stuff
[13] <walla2butterfly> or would the bacteria still not grow fast enough
01[13] <java> walla: you'd have to see if things would balance out for each example
01[13] <java> have to try it out and see
[13] <walla2butterfly> what about proabablity
01[13] <java> every tank is different
[13] <walla2butterfly> so what would be an acceptable amount of ammonia before water change is needed
01[13] <java> if you have large tank with a lot of water, little rock, but still some bioload, you'd probably end up with a nitratye problem
[13] <walla2butterfly> k, just trying to figure out best way to cycle the new tank
01[13] <java> re ammonia: personally, i got alarmed during my cycle if i saw any at all, becaue ammonia really is extremely toxic. my personal highest recorded level was 0.8 pmm. if i were to do this on a larger system i might set my threashold at 1.0ppm
01[13] <java> and TRY to keep it below
01[13] <java> the best laid plans often fail and all that
01[13] <java> but i'd have a goal to work towards
01[13] <java> back to your question, you could try to make up for the lack of rock other ways
01[13] <java> a substantial sandbed
01[13] <java> a deep sand bad
01[13] <java> a remote DSB
01[13] <java> refugium/sump loaded with live rock
01[13] <java> depending on what you'd be willing to accomodate/set up
01[13] <java> if it had to be display only
[13] <walla2butterfly> rock question?
01[13] <java> and i wanted a lot of open room, i'd probably try a deep, but heavily stirred, i.e. lots of snails, brittle stars, worms, sandbed
01[13] <java> yeah, you were wondering about having little rock in a big tank
01[13] <java> you could make up for it with sandbed
[13] <walla2butterfly> was looking at a way to cycle only
01[13] <java> but what about after? you mean add more rock?
[13] <walla2butterfly> yes gradually
01[13] <java> i think you should add all the rock you intend to keep at one time
[13] <walla2butterfly> k back to changing water,
[13] <walla2butterfly> LOL
[13] <walla2butterfly> what do you think of cycle with not all the water? Just enough
01[13] <java> that's interesting...
01[13] <java> big tank, maybe filled halfway?
[13] <walla2butterfly> okay back to the lecture, hogging peoples time
01[13] <java> no, this is a good and relevant discussion
[13] <walla2butterfly> something like tht
[13] <walla2butterfly> that
[13] <Rob> agreed
[13] <walla2butterfly> make water changes a little bit easier
01[13] <java> and i think i've said what i needed to say regarding microenvironments as it related to biofilms, sandbed, and live rock
01[13] <java> yeah, i like your idea
[13] <walla2butterfly> was very interesting chat today, put a lot of things together
01[13] <java> because if you DO get a bigger spike than you could handle by changing, you could jsut pour water in to dilute it
01[13] <java> thank you
[13] <Rob> This would save the water change
[13] <walla2butterfly> what role is my current LR going to play in the cycle
01[13] <java> yeah... because the tricky thing about a 75% water change is that you have to be super careful about temp and slinity
01[13] <java> but pouring waer in is differnt
01[13] <java> water
01[13] <java> i liek your idea
[13] <Rob> Good thoughts so you can add the fresh water gradually to keep these stable?
[13] <walla2butterfly> and hopefully cycled before it is full
01[13] <java> well, i meant pour in mixed saltwater, but if your only addin say 20% of the volume to lower a spike, it doesn't have a big impact if the temp is off by 2 or 3 degrees, or by .002-3 SG
[13] <Rob> I meant fresh saltwater
01[13] <java> whoops, yeah, exactly
01[13] <java> this is why i wish more people would come to chat
01[13] <java> i get ideas form others too
[13] <walla2butterfly> yea fresh freshwater would be a whole different problem rising LOL
01[13] <java> and it jsut contributes to the whole classes experience
01[13] <java> nice chat today!
[13] <walla2butterfly> great
[13] <Rob> Totally agree thanks a lot
01[13] <java> it's 2 PM and today i really have to run
[13] <walla2butterfly> so next weeks subject
01[13] <java> you're all very welcome
02[13] * Rob ([email protected]) Quit (Quit: Leaving)
01[14] <java> next week is going to be applications on the nitrogen cycle, starting off looking at things to augment natural setups
[14] <walla2butterfly> TY, have a great day.
01[14] <java> my pleasure, you too!!
01[14] <java> take care mchia!
01[14] <java> thanks for coming and participating!
03[14] * Retrieving #micro08 modes...
[11] <mchia> Maybe some of them are in the chemistry channel.
01[11] <java> lol - like the first day? or is it scheduled for the same time?
[11] <walla2butterfly> maybe thought they were doing wes
[11] <walla2butterfly> yes
01[11] <java> that chat is the same time?
[11] <walla2butterfly> but you answered that question on the forum, so they should no
[11] <walla2butterfly> read that chem was doing chat on wes evenings
01[11] <java> oh, got worried
[11] <walla2butterfly> wrong "no" Know
[11] <mchia> It's from 10 to 12 EST
01[11] <java> ah
01[11] <java> thanks mchia
[11] <mchia> I'm also on it now
[11] <walla2butterfly> do you like it is it worth it
[11] <mchia> the chemistry channel
01[11] <java> are there people there?
[11] <mchia> 6 including me & instructor
03[11] * Rob ([email protected]) has joined #micro08
01[11] <java> wow - and it's not even scheduled time an people are there in that chat channel??
[11] <walla2butterfly> hi Rob
01[11] <java> hi rob
[11] <Rob> hi, I'm actually trying to balance to channels
01[11] <java> are you in chem as well?
[11] <walla2butterfly> tell them to get their but... to class
[11] <Rob> yes
01[11] <java> wait - so is chemistry chat scheduled for today or wed? is that chat right now impromptu or scheduled?
[11] <walla2butterfly> I wasnt sure whether it was worth another 75 bucks, and I have looked at the material seems kind of elementry,
[11] <mchia> It's scheduled.
[11] <mchia> They changed it to today
01[11] <java> ok, i guess that explains the low turnout
[11] <mchia> Wade said students can use two windows for both channels
[11] <Rob> The chat gets deeper then the reading material
[11] <walla2butterfly> was wondering about that
[11] <walla2butterfly> maybe I will join then
[11] <walla2butterfly> maybe get a clearnce deal seeing how it is half over
01[11] <java> well i guess we'll start anyhow
[11] <walla2butterfly> k
01[11] <java> start talking about microbial habitats and their considerations
01[11] <java> which will logically lead to manipulation for our tanks
[11] <mchia> OK
01[11] <java> some basic considerations are 1) oxygen levels
01[11] <java> because obviously control of these leads to control of various steps of the nitrogen cycle
01[11] <java> for example, proving anaerobic microenvironments can help facilitate denitrification
01[11] <java> another which is still a consideration, but somewhat limited in a reef aquarium
01[11] <java> is temperature
Session Close: Sat Jan 26 11:27:40 2008
Session Start: Sat Jan 26 11:27:40 2008
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Session Close: Sat Jan 26 11:29:02 2008
Session Start: Sat Jan 26 11:30:14 2008
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Session Close: Sat Jan 26 11:30:14 2008
Session Start: Sat Jan 26 11:30:14 2008
Session Ident: #micro08
03[11] * Now talking in #micro08
03[11] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[11] * Set by wade on Wed Dec 31 19:00:01
01[11] <java11> wow sorry
01[11] <java11> not sure what happened
01[11] <java11> got kicked off and a big text box about usage rules
01[11] <java11> anyhow
[11] <walla2butterfly> mmm still listed though
01[11] <java11> hm
01[11] <java11> and this wass the altername nick i provided
01[11] <java11> i'm just going to keep talking on this so as not to waste any time
[11] <walla2butterfly> so limited in a reef
01[11] <java11> we can't do THAT much about temp
01[11] <java11> in a reef, because the limits are very narrow
Session Close: Sat Jan 26 11:32:52 2008
Session Start: Sat Jan 26 11:32:52 2008
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02[11] * Attempting to rejoin channel #micro08
03[11] * Rejoined channel #micro08
03[11] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[11] * Set by wade on Wed Dec 31 19:00:01
01[11] <java> so for example
01[11] <java> say you normally keep things at low 80s
01[11] <java> and you get a death
01[11] <java> and a resulting cyanobacterial bloom
01[11] <java> lowering temp by a few degrees over a couple days could actually make a difference in growth rates
01[11] <java> so that any predators you might have, snails, etc
01[11] <java> could catch up
01[11] <java> other factors in miccrobial habitats are pH
01[11] <java> which isn't manipulated by the aquarist
01[11] <java> but rather by the bacteria themselves to create microenvironments
01[11] <java> and light penetration
01[11] <java> one topic i wanted to get into greater detail with
01[11] <java> is the idea of a concentration gradient
01[11] <java> which isn't in the lecture
01[11] <java> by now we've all realized the idea that there are "anaerobic" and "aerobic" zones
01[11] <java> to use a relevant example
02[11] * java11 ([email protected]) Quit (Ping timeout)
01[11] <java> however, there is rarely a definite line betweent he two zones
01[11] <java> espescially when we start looking at the scale of bacteria , and on a molecular level
01[11] <java> in one of the papers for today
01[11] <java> they get into this idea
01[11] <java> that although on a macroscopic level one might be able to take a O2 sensor
01[11] <java> put it into sand at varying depths
01[11] <java> and determine that there is a delineation at a certain depth in the sand between oxic and anoxic environments
01[11] <java> measure it at "10mm" and call it a day
01[11] <java> if you were to zoom in one the millimeters above and below this "line"
01[11] <java> you'd find, at some scale, a slow lowering of oxygen, along a concentration gradient, as you go down
01[11] <java> at 8 mm you might see half of wht you see at the surface
01[11] <java> at 9mm perhaps 1/4th
01[11] <java> and then at 10mm perhaps not exactly zero, but 1-10%, but lower than the threshold for the probe
01[11] <java> so realize that at some scale there is rarely a definite "line" between 100% and 0% concentration
01[11] <java> always a gradient, a range where the measurement of whatever variable you are interested in becomes lower as the experimental variable changes
01[11] <java> in this case, depth measurement
01[11] <java> so, why do we care?
01[11] <java> well
01[11] <java> because in the case of dissolved oxygen
01[11] <java> and the facilitation of anaerobic microenvironments
01[11] <java> there is a direct application for reefkeeping
01[11] <java> in terms of facilitating denitrification
01[11] <java> because dissolved oxygen is a direct result of things like water agitation and flow
01[11] <java> in a high flow tank, that measured threshold of around 10mm at one flow point
01[11] <java> might be doubled with the higher flow
01[11] <java> if it is high enough
01[11] <java> similarly, one must consider these microhabitats during setup in terms of sand and rock
01[11] <java> using an extreme case
01[11] <java> a bare-bottom tank, with little rock, but high bioload
01[11] <java> and high flow, might have a problem with nitrates
01[11] <java> resulting from the sparsity of anaerobic niches
01[11] <java> at the extreme other end
01[11] <java> a low bioload, low flow tank with a substantial sandbed and a lot of rock
01[11] <java> would likely never have any measurable nitrates in the water column
01[11] <java> by low bioload, that also means free of detritus
01[11] <java> so depending on one's preferences and goals
01[11] <java> these variable should be considered and manipulated accordingly
01[11] <java> variables
01[11] <java> any questions?
01[11] <java> another variable along these lines of manipulating oxygen content in microbial habitats
01[11] <java> is the substrate itself
01[11] <java> obviously the ability if water to diffuse between the sandbed substrate plays a role
01[11] <java> something like crushed coral for example, with a vary large particle size
01[11] <java> might be aerobic down a couple inches
01[11] <java> and the fact that it contains large spaces might become problematic when trapping detritus
01[11] <java> in this case, any denitrification capacity would be accompllished by any live rock in the system and iside each particle of crushed coral
[11] <mchia> So is substrate size is a way to control oxygen in the substrate?
01[11] <java> yes
[11] <mchia> Thanks.
01[11] <java> np - conversely
01[11] <java> a very fine substrate size has it's own set of considerations
01[11] <java> obviously the particles will fit together much more snugly
01[11] <java> impeding flow of oxygenated water downwards
[11] <walla2butterfly> less o2, more anaerobic guys
01[11] <java> yes
01[11] <java> however, ideally one should strike a balance
[11] <walla2butterfly> does this help in the cycling ?
01[11] <java> during the initial cycle things are sorting out
[11] <walla2butterfly> k
01[11] <java> but the consideratioin i'm discussing
01[11] <java> comes more into play in terms of planning out a long term habitat for bacteria
01[12] <java> considerations
01[12] <java> so when we switch to a really fine substrate
01[12] <java> something else needs to be considered
01[12] <java> which is the formation of biofilms
01[12] <java> bacteria in environment
01[12] <java> frequently facilitate their own space to some degree
01[12] <java> by this i mean that they can sort of "build their own house"
01[12] <java> and lilve in communitites
01[12] <java> live
01[12] <java> in the lecture presentation
01[12] <java> there was an illustration of formation and structure of biofilms
01[12] <java> bacteria in nature
01[12] <java> frequently are encapsulated
01[12] <java> this capsule whihc they form themselves
01[12] <java> are typically made up of sugars and proteins produced and secreted by the bacteria
[12] <walla2butterfly> which pg for the illustration
01[12] <java> page 8
[12] <walla2butterfly> ty
01[12] <java> in a way, bacteria make their own "clothes" so to speak, this capsule is something they "wear"
01[12] <java> and it serves a simialar function as clothing for humans
01[12] <java> it protects them from their environment
01[12] <java> and it also serves as a matrix by which they can influence the true microenvironment, right up against their "skin" or their cell wall
01[12] <java> many capsules have degradative enzymes which process environmentla substrates
01[12] <java> and there can be enzymes which help to keep a specific, fine-tuned pH nearby as well
01[12] <java> it's actually more like a space-suit than regular clothing
[12] <walla2butterfly> so make their own environment in a way??
01[12] <java> because it is "active"
01[12] <java> yes, to a certain degree
01[12] <java> but it's also limited by the true environment around them
[12] <walla2butterfly> right they probably can only control so much
01[12] <java> exactly
01[12] <java> so, enters the biofilm
01[12] <java> bioifilms are like little towns and cities, communities of bacteria
01[12] <java> where they stay together after multiplyng
01[12] <java> their capsules become spatially intertwined
01[12] <java> some bacteria dies, but their capsules and dead cells don't really physically leave, but get incorporated into the interstitial matrix between cells
[12] <walla2butterfly> (takes a village to raise a bacteria, LOL. sorry couldnt helpit)
01[12] <java> lol
01[12] <java> and when these things really become established, a film visible to the naked eye can form
01[12] <java> a biofilm
01[12] <java> it may just feel like a slimy coating
01[12] <java> but it's actually a bacterial community
01[12] <java> so getting back to what i was talking about regarding grain sizes
[12] <mchia> Once you can see it, does it become a microbial mat?
01[12] <java> yes, when these thigs grow undisturbed for a long time, they become microbial mats
[12] <walla2butterfly> what is the diff between the bioflim and mat
01[12] <java> the lower depths of microbial mats actually harden and become rocklike
[12] <walla2butterfly> k
01[12] <java> and true "mats" are really really old
01[12] <java> on the order of centuries/millenia
[12] <walla2butterfly> like how old?
[12] <walla2butterfly> okay
[12] <walla2butterfly> so we wouldnt have mats in our tanks
01[12] <java> it's the microbial version of a reef
01[12] <java> no
[12] <walla2butterfly> gotcha
01[12] <java> but it's like a reef in that the reef foundation is coral skeleton form thousand of years ago
01[12] <java> from thousands
[12] <walla2butterfly> okay grain size
01[12] <java> in a small grain size
01[12] <java> because of how tightly fitting the grains are
01[12] <java> microbial communities from neighboring grains can form intertwined biofilms more readily
01[12] <java> if you look at a typical oolite sandbed, against glass
01[12] <java> you can resolve visually the grains because there's visible space between them
01[12] <java> and bacterial communities will only intertwine with others they can physically touch
01[12] <java> but with a fine powdery sand
01[12] <java> the entire sandbed can become an intertwined bacterial community
01[12] <java> and along with the aragonite dissolution and subsequent precipitation that can cause sandbeds to "fuse" or harden
01[12] <java> then one can visualize where the majority of the sandbed might become dangerously immobile, and anoxic
[12] <walla2butterfly> ?
01[12] <java> the
01[12] <java> "gradient" i described earlier would be closer to the surface
[12] <walla2butterfly> so not to fine either
[12] <mchia> So if the sand bed fuses, it can be a bacterial problem?
01[12] <java> because biofilms are on inspection an actual physical goo
01[12] <java> which is thicker than water
[12] <walla2butterfly> so too much no water ( environment)
01[12] <java> then oxygen diffuses even more slowly than if what wass between the grains was jsut water
01[12] <java> right
01[12] <java> the dissolved oxygen not only may diffuse slower, but not at all, ever
01[12] <java> if there's an actual physical blockage composed of hardened sandgrains and think goo where there might normally be a little space for water
01[12] <java> thick
01[12] <java> it's all about middle ground
01[12] <java> you want to facilitate a biofilm
[12] <walla2butterfly> thinking stinking mud?
01[12] <java> but not one that gets so thick that water can't ever penetrate
01[12] <java> yep! it'll defintiely get stinky
01[12] <java> and don't forget what we covered in another chat
01[12] <java> that just because water can get through
01[12] <java> it does NOT mean that water is oxygenated
01[12] <java> because it gets consumed by bacteria as it circulates downwards, and this consumption depletes the water of oxygen rather quickly
01[12] <java> so the anoxic, anaerobic habitats aren't because water doesn't circulate
01[12] <java> but because it circulates slowly enought through the bed that it can get consumed
01[12] <java> so a really anaerobic bed isn't good if water (and thereby nutrients AND WASTE!!) can circulate
[12] <walla2butterfly> the oxygen?
01[12] <java> ah i see
01[12] <java> water circualted slowly enough through the bed that oxygen can get consumed
[12] <walla2butterfly> okay, on the upper level right
01[12] <java> yes, AND along a gradient, the O2 levels will decrease as depth increases
[12] <walla2butterfly> gotcha
01[12] <java> there's ALWAYS a gradient, unless it's somemthing completely imnpermeable like glass or plastic
01[12] <java> but in terms of the surface of live rock
01[12] <java> or a sandbed
[12] <walla2butterfly> right you dont starve to death over night
[12] <mchia> Hence are there also gradients of bacterial types?
01[12] <java> yes - very good
01[12] <java> the aerobic bacteria will find their happiest spots adn grow well there
01[12] <java> some of those same might adapt to different conditions, grow slower, be less populous, but still be ther as you go down
[12] <walla2butterfly> yes there are the ones that can use oxygen or not, and those who could careless if it is there
01[12] <java> right!
01[12] <java> you guys defintely are getting this
[12] <walla2butterfly>
01[12] <java> i think this is a good time for a 10 minute break
[12] <walla2butterfly> k
01[12] <java> but first, any other questions?
01[12] <java> ok, i'll be back by 12:47
[12] <walla2butterfly> or 9:47
[12] <walla2butterfly> so rob, are you out there
[12] <Rob> yes I'm here
[12] <walla2butterfly> so are you Bob? ( from last week)
[12] <Rob> Yes, the chat wouldn't let me sign on with the same name on two channels.
[12] <walla2butterfly> okay was wondering if it was the same, but I actually had a ? for you but for the life of me I cant remember what it was. Have to work on that
[12] <Rob> I've been out of town at business meeting so now I'm trying to catch up.
[12] <walla2butterfly> kind of interesting stuff , dont you think, or is stuff you already knew
[12] <Rob> It's stating to take the aquarium to a new level for me
[12] <walla2butterfly> I hear that stuff I never thought about before. Your in the chemistry also
[12] <Rob> The chemistry is good but it's still at the basic level. I'm hoping it evolves like this one.
[12] <walla2butterfly> think it is worth joining ( paying) at this point?
[12] <walla2butterfly> heard the lecture/chat is more involved
[12] <walla2butterfly> I have looked at the lit, seemed pretty elementry
[12] <Rob> As far as catching up no problem. The chats go into some good tank problem solving.
[12] <walla2butterfly> do they post the old chats?
[12] <Rob> At this time I would say chem=high school level & this one is definately=college.
[12] <Rob> Yes they do
[12] <walla2butterfly> have to think about it
[12] <walla2butterfly> harder that is
[12] <Rob> Mchia, you're in both. What do you think?
[12] <walla2butterfly> we were talking about it at the beginning before you joined, that is where I heard the chats were good
[12] <mchia> The other chat is more a discussion
[12] <Rob> agreed
[12] <mchia> This is more of a lecture
[12] <walla2butterfly> do they use the forum
[12] <mchia> Not really.
01[12] <java> that's what i'm curious about
[12] <walla2butterfly> I like the lecture breaks down the reading and sums it up
01[12] <java> i'm surprised more people don't use the forum
[12] <mchia> Maybe that's why it's more of a discussion
[12] <mchia> on the chemistry side
[12] <Rob> True I'm posting an issue today. Maybe it'll give more life to the forum.
01[12] <java> ah, thank you
01[12] <java> i said in one of the threads we need a TROLL!
01[12] <java> someone to get everyone riled up
[12] <walla2butterfly> so I am curious about the rock you were about to talk about
[12] <walla2butterfly>
01[12] <java> i was on another forum and someone posted about how you really SHOULD pee in your tank to cycle it and the topic exploded
[12] <walla2butterfly> obvious I am not a troll, dont have the hair for it
01[12] <java> no - a forum troll is someone who makes a post to get peoplpe annoyed
01[12] <java> people
[12] <Rob> I heard about that cycling method.
01[12] <java> yeah, it's out there
01[12] <java> oh right - the rock
01[12] <java> let's think for a scond what "live rock" really is
01[12] <java> second
01[12] <java> it's the old skeleton of dead coral
01[12] <java> and if you've ever taken a look at a freshly deceased coral skeleton
01[12] <java> you'd see that it's highly porous, highly structured
01[12] <java> as an animal skeleton, there are a lot of specialized structures
01[12] <java> nooks, holes, and the calcium carbonate is REALLY porous if you were to look at it under a dissecting scope
01[12] <java> this is basically the underlying structure of what we're dealing with
01[13] <java> once it
01[13] <java> it's dead,
01[13] <java> as in the rest of nature, the dead space quickly becomes filled with life
01[13] <java> at the level we're considering, it's a GREAT structure for biofilm formation, with the films covering the insides of pores, the surfaces of specialized skeletal structures, etc.
01[13] <java> obviously ther's other life to consider
01[13] <java> protists
01[13] <java> small animals like worms
01[13] <java> algaes, coraline and macro
01[13] <java> all colonize these surfaces
01[13] <java> if you've ver broken up live rock to make it fit in the aquarium
01[13] <java> you'll see tunnels from the larger worms
01[13] <java> and sometimes localized areas deep within of a black or rusty color
[13] <mchia> What kinds of worms?
01[13] <java> bristleworms, eunicids, fanworms, all dig into the rock
[13] <mchia> Tube worms or bristle worms?
01[13] <java> yep
[13] <mchia> OK
01[13] <java> eunicids actually tunnel in, adn can be quite long
01[13] <java> and
01[13] <java> and they live such a reclusive life that you may not even know they're there unless you crack open a rock
01[13] <java> suffice to say, live rock is very, very "alive"
[13] <walla2butterfly> eunicids= are they what they call "peanut worms"?
01[13] <java> i'm not sure about nicknames
[13] <walla2butterfly> k
01[13] <java> they're scary looking, have scrapers which can burrow through calcium carbonate, look like they'd take off a pinky
[13] <walla2butterfly> ugh
01[13] <java> on the really big ones
01[13] <java> i saw pics somewhere of someone who found one 3 feet long in a not huge system
01[13] <java> can't remember how big
[13] <walla2butterfly> WOW
01[13] <java> yeah, when he found it he said he nearly peed his pants lol
[13] <walla2butterfly> "girlie"face and chills (here)
01[13] <java> lol
[13] <mchia> I think they are called bobbit worms
[13] <Rob> peanut worms are sipunculids
[13] <walla2butterfly> ty
01[13] <java> thanks!
01[13] <java> anyhow, all these organisms play a role
01[13] <java> and the structures i've mentioned play a role as well
[13] <walla2butterfly> never thought about a bigger tank for my worms ( think he will buy into it)
01[13] <java> coral skeletons near the surface of rock is very porous
01[13] <java> and these pores function in a manner analogous to the spaces of between grain of sand which we've already discussed
01[13] <java> so it's possible to form a gradient of oxygen between the surface and deeper down
01[13] <java> as well as provide a nice physical sructure for biofilm formation
01[13] <java> but with the rock, because the type/quantity of life is greater than sand
01[13] <java> biofilm thickening and hardening is less likely
01[13] <java> because physical niches may be occupied by other organisms
01[13] <java> whereas the sand bed really is the domain for bacteria
01[13] <java> but you also have to picture the physical substrate a little differently than a sandbed
01[13] <java> when considering gradients
01[13] <java> a sandbed is fairly uniform at it's surface, flat
01[13] <java> the gradient follows the contours of the sand as it rises and falls
01[13] <java> because the depletion of oxygen under conditions of O2 levels and flow are fairly constant, if the sand is uniform across the tank
01[13] <java> similarly, these O2 gradients in live rock will also follow the contours of the rock, across all nooks and crannies, but also IN THE TUNNELS
01[13] <java> oxygenated water will be able to enter the rock itself via some of the tunnels
01[13] <java> sometimes going quite deep
01[13] <java> or completely through
[13] <Rob> So the live rock has a large surface area
01[13] <java> however, this doesn't mean that the entire inside of the rock is oxygenated
01[13] <java> Rob - yes
01[13] <java> but the gradient will vary depending on the O2 levels in water traveling through the pores
01[13] <java> and tunnels
01[13] <java> now considering that most rock *probably* isn't as penetrable as a sandbed
[13] <walla2butterfly> lower on the rock closer to the sand would be less O2?
01[13] <java> if it were actually sitting on the sand then yes, at the area actually restricted from flow
[13] <walla2butterfly> k
01[13] <java> *probably*, because there is a great variety out there of rock and sand
[13] <mchia> How about if the rock was partially buried?
01[13] <java> there's lace rock, and seeded terrestrial rock like from Tampa Bay Saltwater
01[13] <java> lace rock being so porous that it might not actually support any anaerobic niches at all
01[13] <java> and the hard, non-porous seeded terrestrial rock isn't porous because it isn't made up of structured coral skeleton, but solid rock crystals
[13] <walla2butterfly> interesting
01[13] <java> so those are the extremes, and people actually use a lot of different thinngs for their LR, or somemtimes "base rock"
[13] <walla2butterfly> about the seeded rock
01[13] <java> all have varying capacities for life and for supporting denitrification
01[13] <java> oh, the seeded rock
[13] <walla2butterfly> well its all interesting
01[13] <java> yeah, so harvesting of carribean/florida reefs is prohibited
01[13] <java> so TBS dumps rock into the oceam, lets it sit for a few years during which it gets colonized
[13] <walla2butterfly> have read that and they claim it is the same but obviously not
01[13] <java> I've seent their rock and it's VERY ful of life - at the surface
01[13] <java> full
01[13] <java> very pretty stuff
01[13] <java> but although i've never used it, i suspect it can't be very good for biological filtration
01[13] <java> as live rock is typically used for
01[13] <java> so again, these considerations are important for setup
01[13] <java> when you're thinking about what you want to keep
01[13] <java> and designing a habitat to support it, biologically
[13] <walla2butterfly> and being as natural in bio as possible
01[13] <java> yeah - i'm a big proponent of a really deeply thought out system on the biological end
01[13] <java> and just letting it do it's own thing
01[13] <java> set it up, do water changes and prune
01[13] <java> but not much else
01[13] <java> because really, the less you futz with a tank, the happier the inhabitants, i.e. corals seem to be
01[13] <java> I set up my tank in September
[13] <walla2butterfly> some say you should change out some LR every now and then?
01[13] <java> well... i think that depends
01[13] <java> botgh on how things hahve been going and timeframe
01[13] <java> both
[13] <walla2butterfly> they say to reguvinate the tank
01[13] <java> well, here's the thing
01[13] <java> one reason i like the soft cycle is because it preserves the original diversity as much as possible
01[13] <java> on a reef things are really competitive for space
01[13] <java> BUT
01[13] <java> a lot of people who use the traditional method for cycling and curing rock
01[13] <java> well, curing, really
01[13] <java> of sticking it in a bucket, letting things die and rot, the "bucket of death" lol
01[13] <java> kills off SO much life
[13] <walla2butterfly> you end up with an uneven balance?
01[13] <java> and what you end up with is a micro-ecosystem out of balance once things recover
01[13] <java> HAHA veryy good
01[13] <java> yeah, and when things grow back, the competition is gone
[13] <walla2butterfly> TY, so in sept, your tank
01[13] <java> things become predominant that shouldn't be
01[13] <java> oh, right, i was saying that after the first 2 weeks, my hands have been in my tank maybe 3 times, and i haven't moved a frag or rock AT ALL
01[13] <java> because i think that corals grow best when they aren't disturbed
01[13] <java> they're not used to being moved around
01[13] <java> they sit in one place and grow foe 300 years
01[13] <java> for
[13] <Rob> With an existing tank, can you softcycle LR in a seperate tank and then add it to the main tank when the levels drop?
01[13] <java> yeah, i think that would be a great way to make it more practiccal
01[13] <java> the reason i brought up my tank wass just to illustrate that i like to think about setup and placement, set it up, then jsut not mess with it
01[13] <java> at all
[13] <walla2butterfly> always QT my LR,so I guess in a way I do soft cycle them
01[13] <java> as long as you don't let ammonia spike it would still be tecjhnically a "soft cycle"
01[13] <java> one other note
01[13] <java> people think that you *NEED* that ammonia spike to "get things going"
01[13] <java> not true
01[13] <java> the nitrogen cycle is ubiquitous - it's going on all around us, all the time
01[13] <java> in oceans, ponds, lakes
01[13] <java> BUT ALSO
01[13] <java> in the soil in your yard, even in a crack between the sidewalk
01[13] <java> everywhere
01[13] <java> what this means is that the nitrogen cycle is "unbreakable"
01[13] <java> things just always balance out
01[13] <java> it's can't not balance out, it's the natural order of things
01[13] <java> and additionally, you don't need to add any external sources of ammonia to get ammonia in a new system
[13] <walla2butterfly> ?
01[13] <java> because ammonia comes from the breakdown of all living materal
01[13] <java> if your'e adding live rock, there's going to be detritus on it
[13] <walla2butterfly> so if you put "dead" sand in a tank it would still produce some ammonia
01[13] <java> it's going to come with things like pods and worms, and there is always going to be a certain amount that dies off from the trip from the reef to your tank
[13] <walla2butterfly> and would it produce the right kind of bacteria
[13] <mchia> What if you sterilize it?
01[13] <java> it produced food for the bacteria, in the form of ammonia
01[13] <java> if you were to buy live rock and sterilize it, you'd kill everything and would have a lot of dead matter
01[13] <java> you'd get a massive ammonia spike
[13] <walla2butterfly> what if it was a large tank ( lots of water) and small rock, would you be okay with the ammonia and then slowly add stuff
[13] <walla2butterfly> or would the bacteria still not grow fast enough
01[13] <java> walla: you'd have to see if things would balance out for each example
01[13] <java> have to try it out and see
[13] <walla2butterfly> what about proabablity
01[13] <java> every tank is different
[13] <walla2butterfly> so what would be an acceptable amount of ammonia before water change is needed
01[13] <java> if you have large tank with a lot of water, little rock, but still some bioload, you'd probably end up with a nitratye problem
[13] <walla2butterfly> k, just trying to figure out best way to cycle the new tank
01[13] <java> re ammonia: personally, i got alarmed during my cycle if i saw any at all, becaue ammonia really is extremely toxic. my personal highest recorded level was 0.8 pmm. if i were to do this on a larger system i might set my threashold at 1.0ppm
01[13] <java> and TRY to keep it below
01[13] <java> the best laid plans often fail and all that
01[13] <java> but i'd have a goal to work towards
01[13] <java> back to your question, you could try to make up for the lack of rock other ways
01[13] <java> a substantial sandbed
01[13] <java> a deep sand bad
01[13] <java> a remote DSB
01[13] <java> refugium/sump loaded with live rock
01[13] <java> depending on what you'd be willing to accomodate/set up
01[13] <java> if it had to be display only
[13] <walla2butterfly> rock question?
01[13] <java> and i wanted a lot of open room, i'd probably try a deep, but heavily stirred, i.e. lots of snails, brittle stars, worms, sandbed
01[13] <java> yeah, you were wondering about having little rock in a big tank
01[13] <java> you could make up for it with sandbed
[13] <walla2butterfly> was looking at a way to cycle only
01[13] <java> but what about after? you mean add more rock?
[13] <walla2butterfly> yes gradually
01[13] <java> i think you should add all the rock you intend to keep at one time
[13] <walla2butterfly> k back to changing water,
[13] <walla2butterfly> LOL
[13] <walla2butterfly> what do you think of cycle with not all the water? Just enough
01[13] <java> that's interesting...
01[13] <java> big tank, maybe filled halfway?
[13] <walla2butterfly> okay back to the lecture, hogging peoples time
01[13] <java> no, this is a good and relevant discussion
[13] <walla2butterfly> something like tht
[13] <walla2butterfly> that
[13] <Rob> agreed
[13] <walla2butterfly> make water changes a little bit easier
01[13] <java> and i think i've said what i needed to say regarding microenvironments as it related to biofilms, sandbed, and live rock
01[13] <java> yeah, i like your idea
[13] <walla2butterfly> was very interesting chat today, put a lot of things together
01[13] <java> because if you DO get a bigger spike than you could handle by changing, you could jsut pour water in to dilute it
01[13] <java> thank you
[13] <Rob> This would save the water change
[13] <walla2butterfly> what role is my current LR going to play in the cycle
01[13] <java> yeah... because the tricky thing about a 75% water change is that you have to be super careful about temp and slinity
01[13] <java> but pouring waer in is differnt
01[13] <java> water
01[13] <java> i liek your idea
[13] <Rob> Good thoughts so you can add the fresh water gradually to keep these stable?
[13] <walla2butterfly> and hopefully cycled before it is full
01[13] <java> well, i meant pour in mixed saltwater, but if your only addin say 20% of the volume to lower a spike, it doesn't have a big impact if the temp is off by 2 or 3 degrees, or by .002-3 SG
[13] <Rob> I meant fresh saltwater
01[13] <java> whoops, yeah, exactly
01[13] <java> this is why i wish more people would come to chat
01[13] <java> i get ideas form others too
[13] <walla2butterfly> yea fresh freshwater would be a whole different problem rising LOL
01[13] <java> and it jsut contributes to the whole classes experience
01[13] <java> nice chat today!
[13] <walla2butterfly> great
[13] <Rob> Totally agree thanks a lot
01[13] <java> it's 2 PM and today i really have to run
[13] <walla2butterfly> so next weeks subject
01[13] <java> you're all very welcome
02[13] * Rob ([email protected]) Quit (Quit: Leaving)
01[14] <java> next week is going to be applications on the nitrogen cycle, starting off looking at things to augment natural setups
[14] <walla2butterfly> TY, have a great day.
01[14] <java> my pleasure, you too!!
01[14] <java> take care mchia!
01[14] <java> thanks for coming and participating!
03[14] * Retrieving #micro08 modes...
