what do anaerobic bacteria eat ?

[Snarkys]

Im curious what anaerobic bacteria eat .

I was under the assumption that the anaerobic bacteria in our DSB's and remote DSB's were actually eating the some of the nitrate in our systems, however this turns out not to be the truth. Looks like they are utilizing the presence of oxygen in the nitrate and when they remove the oxygen molecule it turns nitrate into nitrogen gas.

Feel free to correct me if i am understanding this wrong but my question is, what is it that the anaerobic bacteria are eating in our DSBs and remote DSBs ?

 

[mesocosm]

Re: what do anaerobic bacteria eat ?

<a href=showthread.php?s=&postid=8390692#post8390692 target=_blank>Originally posted</a> by Snarkys
Im curious what anaerobic bacteria eat . ...

What bacteria "eat" is largely dependent on the specific strain of bacteria being discussed ...

Most bacterial species uutilize simple monomeric substances such as sugars or amino acids as growth substrates, whereas others digest complex proteins and polysaccarides. Although some bacteria, such as Pseudomonas cepacia, can utilize any one of over 100 different carbon-containing compounds for growth, most organisms can utilize only a limited number. Other microbes are restricted to growth on only one or a few chemically related substances. ...

Extracted from:
Isolation, Nutrition, and Cultivation of Microorganisms
Part II Microbial Physiology: Nutrition and Growth
http://www.sinauer.com/perry/MicrobialLife05.pdf

But it's not just about where bacteria obtain the substances necessary for physical growth, they also need to acquire energy. The concept of electron "donors and acceptors" is critical to an understanding of this ... and goes right to the heart of your question about what anaerobes are "eating" in a DSB ...

Electron Donor

An electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process.

Electron donors give up or donate an electron during cellular respiration, resulting in the release of energy. Microorganisms, such as bacteria, obtain energy to grow by transferring electrons from an electron donor to an electron acceptor. The microorganism through its cellular machinery collects the energy for its use. The final result is the electron is donated to an electron acceptor. During this process (electron transport chain) the electron donor is oxidized and the electron acceptor is reduced. ...

Electron Acceptor

An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that, by virtue of its accepting electrons, is itself reduced in the process.

A terminal electron acceptor is a compound that receives or accepts an electron during cellular respiration or photosynthesis. Microorganisms such as bacteria obtain energy to grow by transferring electrons from an electron donor to an electron acceptor. The microorganism through its cellular machinery collects the energy for its use. The process starts with the transfer of an electron from an electron donor. During this process (electron transport chain) the electron acceptor is reduced and the electron donor is oxidized. Examples of acceptors include oxygen, nitrate, iron (III), manganese (IV), sulfate, carbon dioxide ...

Extracted from Wikipedia

For a more detailed and comprehensive reference listing of what is specifically going on with anaerobes in a DSB, this one is a true classic, and despite it's length and "tangent wanderings", is a "must read". Be prepared for a little cyber-digging ... this one is still up and running with the latest post dated 1.16.2006 (yep, over two years old with 71 pages and still counting) ... but it's well worth the effort.

DSB Related Journals, Newspaper Articles, ETC...
RC Thread, Reef Discussion Forum
(Yellotang, 11.1.2003)
http://www.reefcentral.com/forums/showthread.php?s=&threadid=263482&highlight=zeovit




For a generalized overview of what bacteria "eat" ... and how they're utilizing what they consume ... I've found these two to be useful:

Isolation, Nutrition, and Cultivation of Microorganisms
Part II Microbial Physiology: Nutrition and Growth
http://www.sinauer.com/perry/MicrobialLife05.pdf

Microbial Biofilms: from Ecology to Molecular Genetics
Mary Ellen Davey and George A. O'toole
Microbiology and Molecular Biology Reviews
December 2000, p. 847-867, Vol. 64, No. 4
http://mmbr.asm.org/cgi/content/ful...rnals.asm.org/cgi/search&journalcode=mmbr#top




JMO ... HTH
:thumbsup:

 

[Snarkys]

ok, its pretty rare that i get a response this helpful

thanks : )

 

[mesocosm]

:thumbsup: :thumbsup: :thumbsup:

 

[DrBegalke]

Single celled organisms don't really "eat" in the sense that large organisms do, this article is pretty good as well:

http://dwb.unl.edu/Teacher/NSF/C11/...c.edu/microtextbook/metabolism/RespAnaer.html

 

[MCsaxmaster]

Very nice Mesocosm :thumbsup:

In a nut shell they are digesting and consuming carbon-rich molecules, usually from detritus they are decomposing. The detritus provides energy (carbon) and structural components (N and P). Aerobes like us breath in oxygen. Anaerobic bacteria transform nitrate into oxygen and nitrogen gas, "breath" the oxygen and ditch the N2.

Chris

 

[mesocosm]

What's up, Chris? Are you folks back in continental North America yet, or are you still having demasiada diversion with tropical storms in the Caribbean?

For those of you who are not familiar with some of Chris' recent publications, you might want to check out the following articles ... they provide much needed "context" for the discussion of what bacteria "eat" ...

The Nutrient Dynamics of Coral Reefs:
Part I, Biogeochemical Cycles
Chris Jury
Reefkeeping Magazine
August, 2006
http://reefkeeping.com/issues/2006-08/cj/index.php

The Nutrient Dynamics of Coral Reefs:
Part II, The Oceanic System
Chris Jury
Reefkeeping Magazine
October, 2006
http://reefkeeping.com/issues/2006-10/cj/index.php

Excellent stuff ! ... :thumbsup:


Apologies if what follows veers too far off topic, but anaerobes don't exist in isolation ... they are but one component of a diverse microorganism community. Oftentimes, the O2 depleted microenvironment which they require is generated by other members of that community. A brief look at what's going on with the other members of their community may be useful. Consider ...

Interestingly many of the most studied microorganisms are chemoheterotrophs. One may get the mistaken sense that this means that chemoheterotrophs are the most common microbes in the environment and this is probably pretty far from the truth. Autotrophy and photosynthesis are very common metabolic activities and dominate a large number of habitats from the open ocean to deep in the earth.

Extracted from:
Micro Textbook
http://www.bact.wisc.edu/Microtextb...ons&file=index&req=viewarticle&artid=4&page=1

The emergent academic research literature suggests that the saltwater hobbyist-industry model which presents the "heterotrophs"-Nitrobacter-Nitrosomonas bacterial guild as a definitive description of what's going on in marine aquaria ... is disturbingly incomplete. Useful ... to be sure ... but fundamentally incomplete. Examples of types of bacteria that need to be included in "the discussion" are cyanobacteria (not as a "nuisance", but as a major player in nutrient cycling and coral nutrition), and PSB (photosynthetic bacteria).

JMO ...


Digging through some of my old references, I came across some culture media components for cyanobacteria and Nitrosomonas species ...

A growth medium for Cyanobacteria.

MgSO4 - 7H2O: Source of magnesium and sulfur
CaCl2 - 2H2O: Source of calcium
NaCl: Source of sodium
K2HPO4: Source of potassium and phosphate
NaCO3: Source of carbon
Ferric ammonium citrate: Source of iron

Micronutrient requirements of growth medium for Cyanobacteria.

H3BO3
MnCl2 - 4H2O
ZnSO4 - 7H2O
NaMoO4 - 2H2O
CuSO4 - 5H2O
Co(NO3)2 - 6H2O

A growth medium for Nitrosomonas.

(NH4)2SO4: Energy source. nitrogen source, sulfur source
MgSO4 - 7H2O: Source of magnesium
CaCl2 - 2H2O: Source of calcium
CaCO3: Source of carbon and calcium
KH2PO4: Source of phosphorous, buffer
Fe-EDTA: Source of iron

See anything familiar in terms of the stuff many of us regularly add (oftentimes as a component of "buffers" and/or "additives") to our systems? ...

... you should ...

Kind of helps to explain why systems with "perfect" water chemistry test results and appropriate flow can still experience cyanobacteria outbreaks, doesn't it? ...

...


My point is that with regards to the bacterial guild in a captive marine ecosystem ... everything is connected. Once you scratch below the surface layer, it's incomplete to talk what anaerobes are "eating", without also taking into consideration what the rest of the bacterial guild is "eating" ... and what other strains in the guild are doing with what is respired and excreted.


One bacterium's "poo" ... is another bacterium's feast (especially in a DSB) :eek1: :lol:


JMO
:thumbsup:

 

[MCsaxmaster]

What's up, Chris? Are you folks back in continental North America yet, or are you still having demasiada diversion with tropical storms in the Caribbean?

Yup, we got back ca. 3 weeks ago. Actually, we avoided Ernesto by heading to PR instead of staying in Wilmington. Ironic, no? And for the record, no hay ninguna cosa tal como demasiada diversion

Excellent stuff ! ...

Thanks for the plug

See anything familiar in terms of the stuff many of us regularly add (oftentimes as a component of "buffers" and/or "additives") to our systems? ...

I don't see what you're getting at. Any organism has requirements for these nutrinets. The ions we add with buffers shouldn't be limiting in sea water (though the uptake of these nutrients could be mass transport limited). Adding or not adding buffers, etc. shouldn't directly encourage or discourage the growth of any algae, bacteria, etc. in our tanks.

cj

 

[mesocosm]

<a href=showthread.php?s=&postid=8415271#post8415271 target=_blank>Originally posted</a> by MCsaxmaster
Thanks for the plug

Credit where credit is due ... :thumbsup:

<a href=showthread.php?s=&postid=8415271#post8415271 target=_blank>Originally posted</a> by MCsaxmaster
... though the uptake of these nutrients could be mass transport limited ...

Bingo! ... particularly with regards to cyanobacteria.

 

[MCsaxmaster]

But that would fundamentally disagree with many studies that find cyanboacterial blooms on reefs are strongly correlated with wave energy. If they were mass transport limited in terms of the uptake of whatever nutrients we should expect that increasing water flow should intensify blooms, but the opposite is observed.

 

[mesocosm]

<a href=showthread.php?s=&postid=8416567#post8416567 target=_blank>Originally posted</a> by MCsaxmaster
But that would fundamentally disagree with many studies that find cyanobacterial blooms on reefs are strongly correlated with wave energy. If they were mass transport limited in terms of the uptake of whatever nutrients we should expect that increasing water flow should intensify blooms, but the opposite is observed.

Indeed ... counter-intuitive, isn't it? I think that what is observed is because the concentration gradient of nutrients is oftentimes not the controlling factor of bacterial growth ... but sometimes it is. Let me back up a moment ...

For anyone not familiar with "mass transport", this may be helpful ...

Mass transfer is the phrase commonly used in engineering for physical processes that involve molecular and convective transport of atoms and molecules within physical systems. Mass transfer includes both fluid flow and separation unit operations.

Some common examples of mass transfer processes are the evaporation of water from a pond to the atmosphere; the diffusion of chemical impurities in lakes, rivers, and oceans from natural or artificial point sources; mass transfer is also responsible for the separation of components in an apparatus such as a distillation column.

The driving force for mass transfer is a difference in concentration; the random motion of molecules causes a net transfer of mass from an area of high concentration to an area of low concentration. ...

Extracted from:
http://en.wikipedia.org/wiki/Mass_transfer

So you would expect that increasing flow would simultaneously increase the availability of nutrients. And it does ... but there are other variables involved. The reason that we observe decreased cyanobacteria growth after increasing the flow may not be related to nutrient availability, rather, it may be a function of fluid shear (i.e., the bacteria are being detached and disrupted such that the bacterial community is no longer able to generate a microclimate that facilitates growth). While I haven't found any data pertaining specifically to DSBs (or LR surfaces for that matter), there is data which supports this suggestion regarding the colonisation of marine bacteria in columns of activated carbon ...

Lower cell counts in higher flow regimes are consistent with the findings of Trulear and Characklis (21) that higher flow rate systems have less extensive steady state biofilms because of higher reentrainment of the biofilm by high fluid shear.


Extracted from:
Effects of Surface Area and Flow Rate on Marine Bacterial Growth in Activated Carbon Columns.
Robert J. Shimp and Frederick K. Pfaender
Applied and Environmental Microbiology,
Aug. 1982, p. 471-477

Full Article (pdf)
http://aem.asm.org/cgi/reprint/44/2...ne&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT

BTW ... this article suggests that particle size, surface texture, and the particle's ability to absorb nutrients were significantly more important than the flow rate. Additionally, it has some very cool micrographs.


A moment ago I dropped this in, "the bacteria are being detached and disrupted such that the bacterial community is no longer able to generate a microclimate that facilitates growth". Again, this implies that, in some situations, it's not the nutrients presented within the water column that matters most. I get that from this ...

... The combined effect of reduced flow velocities between the coral branches and its associated fauna are probably the main factors in creating a specific environment more or less independent of the nutritive stage of the surrounding water.

Extracted from:
Evidence of enhanced microbial activity in the interstitial space of branched corals: possible implications for coral metabolism
Christian Schiller and Gerhard J. Herndl
Earth and Environmental Science
Volume 7, Number 4
January, 1989

Source
http://www.springerlink.com/content/jv0n8744743l54t6/

I hasten to note that it's a reasonable criticism to point out that I may be talking about apples and oranges here (DSB communities vs. interstitial communites) ... fair enough, but my point is that the straight up kinetics of mass transfer is not the only variable in what we're observing (hence the variety of observations which initially appear contradictory and at odds with the literature).


But these kinetics are an essential piece of what's going on. While flow rate, surface area, fluid shear, surface texture ... et cetera ... are all potentially critical, nothing is going to grow if the essential elements and compounds are absent. So back to the "buffers and/or additives ... see anything familiar?" thing ...

What I'm suggesting is that, over time, components of the various buffer and additive products gradually accumulate in our systems (see Thiel, Toonen, Bingman, Borneman, and Shimek). These things are well-documented as components of cyanobacteria and marine bacteria growth media ... so the potential to exert significant influence exists and distinct from other cations and anions contained in the various products. Unless actively removed, these slowly increasing nutrients will eventually reach a concentration level where mass transfer kinetics can influence cyanobacteria and marine bacteria growth rates ... sometimes explosively, despite the fact that a water test shows nothing wrong.

Mass transfer ... coming soon to a theatre near you


JMO ... sorry about the length and the hijack, folks

 

[MCsaxmaster]

What I'm suggesting is that, over time, components of the various buffer and additive products gradually accumulate in our systems (see Thiel, Toonen, Bingman, Borneman, and Shimek). These things are well-documented as components of cyanobacteria and marine bacteria growth media ... so the potential to exert significant influence exists and distinct from other cations and anions contained in the various products. Unless actively removed, these slowly increasing nutrients will eventually reach a concentration level where mass transfer kinetics can influence cyanobacteria and marine bacteria growth rates ... sometimes explosively, despite the fact that a water test shows nothing wrong.

How does mass transport come more into play with increasing concentrations of whatever nutrients? The higher the concentration of a substance the less important mass transfer becomes in the uptake of that substance. I have no doubt that many of the impurities and unnecessary additions made with buffers, etc. can build in concentration, but besides N, P and perhaps Fe, which nutrients could possibly be limiting to the growth of cyanobacteria? There is a substantial excess in the availability of most essential nutrients in sea water (e.g. Ca, Mg, SO4, etc.) so increasing their concentration shouldn't positively impact the growth potential of cyanobacteria. N and especially P (and probably Fe in aquariums) are usually considered limiting, though most of the work done on reefs suggests that the concentrations of these nutrients may not actually be important in where cyanobacteria bloom on reefs. Indeed, wave intensity and possibly grazing and competition seem to be much more important factors in determining cyanobacterial blooms on reefs than the concentration of whatever type of nutrient.

Chris

 

[mesocosm]

<a href=showthread.php?s=&postid=8420444#post8420444 target=_blank>Originally posted</a> by MCsaxmaster
How does mass transport come more into play with increasing concentrations of whatever nutrients? ... There is a substantial excess in the availability of most essential nutrients in sea water (e.g. Ca, Mg, SO4, etc.) so increasing their concentration shouldn't positively impact the growth potential of cyanobacteria. ...

Ahhh ... I'm coming at this from a different direction.

I'm talking about what's going on within the microclimate which arises from the attachment/colonisation by cyanobacteria on a porous aquarium surface (such as live rock, or a DSB). The nutrient availability is different compared to availability in the water column. This is what I was getting at with the, "... creating a specific environment more or less independent of the nutritive stage of the surrounding water" excerpt. A portion of the calcium, magnesium, and sulfate ions don't remain dissociated and unbound as they interact with the colony and its microclimate ... they become macro-aggregates. An accumulation of these macro-aggregates gives rise to a nutrient gradient which I consider characteristic of "mass transfer".

If you consider this is a clumsy use of "mass transfer" on my part ... fair enough. What's the better to say it? Keywords would be fine ... as Jake will attest, I have some pretty obssessive-compulsive data-mining habits.

<a href=showthread.php?s=&postid=8420444#post8420444 target=_blank>Originally posted</a> by MCsaxmaster
... but besides N, P and perhaps Fe, which nutrients could possibly be limiting to the growth of cyanobacteria? ...

I'm talking about the "additives" part of my statement now ... biotin, riboflavin, niacin, aspartic acid, alanine, glutamic acid, threonine ... to name but a few. I'm not making a mere end-around arugument that simply distills down to overcoming N limitation ... I'm suggesting that these compounds not only provide an alternative C source and potential electron donors/acceptors, but that they also provide critical resources for enzyme synthesis.

If you want to give me a cyber-whipping for asserting something about an area where the literature is not definitive ... fair enough, and I might actually deserve it because this is one of those areas where the good data is only now beginning to emerge.

But be gentle, because I'm right about this ...

<a href=showthread.php?s=&postid=8420444#post8420444 target=_blank>Originally posted</a> by MCsaxmaster
... Indeed, wave intensity and possibly grazing and competition seem to be much more important factors in determining cyanobacterial blooms on reefs than the concentration of whatever type of nutrient.

Very interesting ... I would have chosen grazing and competition as more important factors than wave intensity, with nutrient limitation "overriding" all three.


To what extent do you think that the implications of the field data need to "translated" in order to account for the differences between reefs and marine aquaria (if at all)?


:thumbsup:

 

[MCsaxmaster]

I'm talking about what's going on within the microclimate which arises from the attachment/colonisation by cyanobacteria on a porous aquarium surface (such as live rock, or a DSB). The nutrient availability is different compared to availability in the water column. This is what I was getting at with the, "... creating a specific environment more or less independent of the nutritive stage of the surrounding water" excerpt. A portion of the calcium, magnesium, and sulfate ions don't remain dissociated and unbound as they interact with the colony and its microclimate ... they become macro-aggregates. An accumulation of these macro-aggregates gives rise to a nutrient gradient which I consider characteristic of "mass transfer".

But it is unlikely that there is much of a gradient of nutrients like these. Ions like Ca are kept at much lower intracellular concentrations than in the external seawater, but cell membranes are not overly permeable to the exchange of such ions without active transport. If the cyanobacteria aren't actively taking up and sequestering these ions, why would we expect a gradient in their concentration?

I'm talking about the "additives" part of my statement now ... biotin, riboflavin, niacin, aspartic acid, alanine, glutamic acid, threonine ... to name but a few. I'm not making a mere end-around arugument that simply distills down to overcoming N limitation ... I'm suggesting that these compounds not only provide an alternative C source and potential electron donors/acceptors, but that they also provide critical resources for enzyme synthesis.

Firstly, I would ask why someone is dumping a lot of vitamins and amino acids in their tank? I realize adding amino acid supplements is catching on, but dumping in vitamins...who does that? To be clear, are you saying that you believe that these amino acid additions (and maybe vitamin additions too?) contribute to the C budget of cyanobacteria? If so what makes you think this? I don't follow in terms of these materials serving as electron donors/acceptors. Would you please clarify what you mean for me? I would definitely agree that some of these substances (especially some vitamins and a few particular amino acids) could be very important in structuring algal and microbial communities. Seasonal phytoplankton successions often are driven by dynamic availability of a vitamin like biotin.

If you want to give me a cyber-whipping for asserting something about an area where the literature is not definitive ... fair enough, and I might actually deserve it because this is one of those areas where the good data is only now beginning to emerge.

Goodness, I hope not to cause any offense. If I thought you didn't have a good head on your shoulders this discussion would not be worthwhile and I wouldn't have bothered addressing these points. I examine other people's arguments rigurously and expect that mine should be examined as closely as this is the only way to get to the truth.

Very interesting ... I would have chosen grazing and competition as more important factors than wave intensity, with nutrient limitation "overriding" all three.

I would have thought the same, but the literature suggests otherwise. In general cyanobacterial abundance on reefs shows a strong negative correlation with wave intensity. There is usually a variable negative relationship with macroalgal abundance and grazing appears very important in some systems. Usually cyanobacterial abundance on reefs shows little correlation to ambient N and P.

To what extent do you think that the implications of the field data need to "translated" in order to account for the differences between reefs and marine aquaria (if at all)?

Hmmm, good question. I think it depends on the specific conditions in question. The principles from one to the other are the same but specific variations can be important. For example, maybe Fe gets used up really fast in tanks leading to Fe limitation of some species and this doesn't happen on most reefs in nature. On the other hand, maybe the species of interest are not Fe limited in either the tank or nature making it a moot point.

Chris

 

[mesocosm]

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
Goodness, I hope not to cause any offense. If I thought you didn't have a good head on your shoulders this discussion would not be worthwhile and I wouldn't have bothered addressing these points. I examine other people's arguments rigurously and expect that mine should be examined as closely as this is the only way to get to the truth.

Prana: Sanskrit word meaning 'breath' and refers to a vital, life-sustaining force of living beings and vital energy in natural processes of the universe.

One of the books I read in one of my web design classes had a quote from a guy who designed high-level internet conferencing systems ... the kinds of systems with rooms which are rigged to be elaborate biometric, physiological response sensors (essentially large lie-detectors with all the visual and graphic bells & whistles). The goal was to fill in the missing spectrum of non-verbal communication which is so important, and yet so absent, when participants are not physically in the same place. The exchange between the author and the guy went something like this ...

The Author: Wow! What you've done is fantastic. It's way beyond what I imagined was technically possible. It's like being in the same room with these people. You can see every subtlety and nuance right there on the monitors.
The Guy: No.
The Author: Really? What's missing?
The Guy: The prana.

Damn internet ... :lol:

Chris, you and I are coming from precisely the same place and I find your rigor quite refreshing ... :thumbsup: :thumbsup:

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... If the cyanobacteria aren't actively taking up and sequestering these ions, why would we expect a gradient in their concentration?

I'm not talking about active uptake by the cyanobacteria ... I'm talking about the gradient(s) which arise from an accumulation in their microclimate. Which gives me an opportunity to post one of my favorite graphics ...

Those little white specks are fluorescent latex beads ... notice how a couple of them have become "stuck" within the matrix of the biofilm? This is the type of accumulation I'm talking about .. the same type of accumulation which some hobbyists choose to address by "rock cooking". If this discussion was about atmospherics, I'd be talking about the Ca, Mg, and SO4 ions as something akin to 'precipitating nuclei'.

Maybe I'm blundering stupidly with the terminology (wouldn't be the first time) ... what's your definition for "mass transfer"?

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... I would have thought the same, but the literature suggests otherwise. In general cyanobacterial abundance on reefs shows a strong negative correlation with wave intensity. ...

Got any links? I'd like to fill in the gaps of my data-mining sweep (which obviously was less good than I thought it was). I get my nutrient gradient preference from this one ...

In this study it was hypothesized that the microbial biomass components change within a few hundred meters as oligotrophic water flows across the reef and becomes enriched with nutrients. ... heterotrophic bacterial biomass increased 4-fold (from 10.1-46.4 mu g C/l), heterotrophic nanoflagellate (HNAN) biomass increased from 4.6-19 mu g C/l, and cyanobacteria from 0.9-4.5 mu g C/l.

Microbial biomass dynamics along a trophic gradient at the Atlantic Barrier Reef off Belize (Central America).
Herndl, GJ
Marine Ecology
Berlin [MAR. ECOL.]. Vol. 12, no. 1, pp. 41-51
1991
http://md1.csa.com/partners/viewrec...&recid=2677450&q=&uid=788483662&setcookie=yes

Perhaps my perspective arises from making too broad of generalizations from what's going on with the heterotrophs, chemolithotrophs, and facultative anaerobes. Any thoughts?

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... Firstly, I would ask why someone is dumping a lot of vitamins and amino acids in their tank? I realize adding amino acid supplements is catching on, but dumping in vitamins...who does that? ...

"Who does that?" ... Gods of the Reef, let's not go there ... hehe ... at least not yet.

BTW ... check out the ingredients of Kent's, Korallin's, Salifert's, Tow Little Fishes' (for example) additives sometime. You might be surprised at how vitamins have penetrated the marine ornamental marketplace. This is to say nothing of the emergent bacterioplankton product lines, but, Gods of the Reef, let's not go there ... hehe ...

... at least not yet ... :lol:

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... To be clear, are you saying that you believe that these amino acid additions (and maybe vitamin additions too?) contribute to the C budget of cyanobacteria? If so what makes you think this? ...

Consider the chemical formulae ... C6H5NO2 (niacin), C17H20N4O6 (riboflavin), C10H16N2O3S (biotin), C5H10N2O3 (glutamine), C3H7NO2 (alanine). Not that these would be primary sources ... but the alternative is excretion, and I have a hard time picturing that.

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... I don't follow in terms of these materials serving as electron donors/acceptors. Would you please clarify what you mean for me? ...

Again ... consider the chemical formulae. I have a hard time visualizing at least some of the C, H, O, N, and S atoms not participating in electron exchange.

<a href=showthread.php?s=&postid=8426592#post8426592 target=_blank>Originally posted</a> by MCsaxmaster
... The principles from one to the other are the same but specific variations can be important. ...

Agreed ... this is why this conversation has the potential to be so informative. The "rub" is in the variations ... which I prefer to call 'dynamics'.


Should we be starting a new thread with this stuff? I'm thinking Snarkys is considering reaching for the phone numbers of the FBI or TSA.


:thumbsup:

 

[MCsaxmaster]

I'm not talking about active uptake by the cyanobacteria ... I'm talking about the gradient(s) which arise from an accumulation in their microclimate. Which gives me an opportunity to post one of my favorite graphics ...

Those little white specks are fluorescent latex beads ... notice how a couple of them have become "stuck" within the matrix of the biofilm? This is the type of accumulation I'm talking about .. the same type of accumulation which some hobbyists choose to address by "rock cooking". If this discussion was about atmospherics, I'd be talking about the Ca, Mg, and SO4 ions as something akin to 'precipitating nuclei'.


If cyanobacteria and other microbes are not sequestering significant amounts of things like Ca, Mg, SO4 etc. (which they are not) and are not dumping these in the environment at a net significant rate (which they are not) they cannot establish a gradient in concentration because these ions aren't particularly going anywhere.

As for the latex bead demonstration, the problem is one primarly of scale. Those beads are maybe 1 um or a few um in size. To say that this is a lot bigger than ions like Ca, Mg, SO4 or even much larger ones like PO4 is a major understatement What this video demonstrates is water flow/diffusional patterns through a microbial film and in a qualitative rather than quantitative way. A bead that gets stuck might simply be stuck and, because it is so much larger than the water molecules and ions that it is travelling with, may not accurately demonstrate water flow or ionic flux in such a situation. If, however, it is accurately demonstrating that water is pooling in such an area this does not indicate that ions are accumulting relative to water. Since the net rate of uptake and release of ions like Ca, Mg, SO4, etc. is negligible such situations of stagnant water cannot represent either accumulation or depletion of these species. Things like N and P which are actively sequestered can definitely become depleted in such a situation but cannot build in concentration as cyanobacteria show a net uptake of such materials, not release.

Maybe I'm blundering stupidly with the terminology (wouldn't be the first time) ... what's your definition for "mass transfer"?

It is, I suppose, simply the movement of energy or material from a fluid onto or within a surface (this implies no mechanism for sequestionration) or off of or without that surface to the fluid (again, no mechanism of release implied) as is controlled by the rate of diffusion through the diffusive boundary layer.

Got any links? I'd like to fill in the gaps of my data-mining sweep (which obviously was less good than I thought it was). I get my nutrient gradient preference from this one ...

Just do a search for something like "cyanobacteria" and "reef" or "Trichodesmium" and "reef" and you should find many papers. The ones that have looked at potential causes for cyanobacterial blooms have found that wave intensity is stongly correlated with the abundance of cyanobacterial mats and that ambient nutrient supply is generally poorly correlated. Most have found abundance of macroalgae and grazing to be of variable importance and to sometimes correlate well with cyanobacterial abundance and other times less well.

Perhaps my perspective arises from making too broad of generalizations from what's going on with the heterotrophs, chemolithotrophs, and facultative anaerobes. Any thoughts?

Microbes are much more abundant around reefs than in the open ocean. The abundance of cyanobacteria and many algae and bacteria is not necessarily correlated with the ambient supply of N and P on reefs, however.

BTW ... check out the ingredients of Kent's, Korallin's, Salifert's, Tow Little Fishes' (for example) additives sometime. You might be surprised at how vitamins have penetrated the marine ornamental marketplace. This is to say nothing of the emergent bacterioplankton product lines, but, Gods of the Reef, let's not go there ... hehe ...

Good lord. Honestly, I don't really pay attention to things like this and never really have. I've never seen any compelling reason to spend a dollar on supplements like these and still don't, so I suppose its not a concern of mine.

Consider the chemical formulae ... C6H5NO2 (niacin), C17H20N4O6 (riboflavin), C10H16N2O3S (biotin), C5H10N2O3 (glutamine), C3H7NO2 (alanine). Not that these would be primary sources ... but the alternative is excretion, and I have a hard time picturing that.

So, you're suggesting that these vitamins are metabolized for energy? Why would any autotroph do that considering the abundant supply of C fixed by photosynthesis, not to mention the generally high concentration of DOC on reefs (especially as compared to the abundance of vitamins). First, I'd like to see some evidence that cyanobacteria (or whatever autotroph) is metabolizing any of these vitamins for energy metabolism. I am extremely skeptical of this, though I am happy to take a look at evidence in favor of this. Second, if these were being used as a C source in energy metabolism what portion of daily respiration can these sources provide? Very, very little I'm certain. I don't think the availabilty of any sort of vitamin is significant in the C budget of any organism, especially not autotrophs. And as for excretion of vitamins--all organisms tend to do this when they have too much, including microbes/algae.

Again ... consider the chemical formulae. I have a hard time visualizing at least some of the C, H, O, N, and S atoms not participating in electron exchange.

Ok, O or S could be used if these vitamins were metabolized, but again where is the evidence that this actually happens? And assuming that it does what portion of the O or S requirements are fulfilled through this pathway? No doubt the high availabilty of O2 and SO4 significantly overwhelm any potential effects here, and we know that O2 and SO4 are used directly by microbes (though it doesn't seem that SO4 reducing bacteria are that abunant in tanks and in fact are usually only abundant in highly organic, extremely anoxic sediment in nature).

Agreed ... this is why this conversation has the potential to be so informative. The "rub" is in the variations ... which I prefer to call 'dynamics'.

Agreed.

Should we be starting a new thread with this stuff? I'm thinking Snarkys is considering reaching for the phone numbers of the FBI or TSA.

Ha, sure, if you like.

Chris

 

[mesocosm]

Chris ... your time and effort is much appreciated ... :thumbsup:

<a href=showthread.php?s=&postid=8434468#post8434468 target=_blank>Originally posted</a> by MCsaxmaster
... So, you're suggesting that these vitamins are metabolized for energy? ...

Heavens, no ... I'm talking about growth ... as in growth factors.

For anyone unfamiliar with some of the "growth factors" involing bacteria, the well-documented categories of growth factors include amino acids, nucleotides, and vitamins. More specifically, C, O, N, H, P (so-called "macro-nutrients); S, Mg, K, Ca, Fe (so-called "micro-nutrients"); "trace elements" (with well-documented metabolic functions) including Co, Zn, Mo, Cu, Mn, and Ni; and vitamins ...

... Most of the vitamins are necessary in central metabolic functions and explains their absolute requirement in many bacteria. Keep in mind that growth factor requirements are species specific, in fact most bacteria need just a few of these compounds or none at all. ... Folic acid, Biotin, Lipoic acid, Mercaptoethane-sulfonic acid, Nicotinic acid, Pantothenic acid, Pyridoxine (B6), Riboflavin (B2), Thiamine (B1), Vitamin B12, and Vitamin K.

Extracted from:
http://www.bact.wisc.edu/Microtextb...ons&file=index&req=viewarticle&artid=3&page=1

Focusing away from photoautotrophs in natural reef systems towards heterotrophs and chemolithotrophs in marine aquaria ... what do you see as the reservoirs of vitamins that heterotrophic and chemolithotrophic bacteria are drawing upon (if any)?

<a href=showthread.php?s=&postid=8434468#post8434468 target=_blank>Originally posted</a> by MCsaxmaster
... in a qualitative rather than quantitative way. A bead that gets stuck might simply be stuck and, because it is so much larger than the water molecules and ions that it is travelling with, may not accurately demonstrate water flow or ionic flux in such a situation. ...

Point well taken ... you see no potential for an accumulation of macro-aggregates immediately adjacent to a bacterial colony (whether autotrophic, or not) to do anything interesting (in terms of gradient formation --> ^ net uptake)?

<a href=showthread.php?s=&postid=8434468#post8434468 target=_blank>Originally posted</a> by MCsaxmaster
... Things like N and P which are actively sequestered can definitely become depleted in such a situation but cannot build in concentration as cyanobacteria show a net uptake of such materials, not release. ...

Do you think that "pulsing" N or P through an aquarium's water column has the potential to generate a transient gradient which would temporarily increase net uptake?

<a href=showthread.php?s=&postid=8434468#post8434468 target=_blank>Originally posted</a> by MCsaxmaster
Good lord. Honestly, I don't really pay attention to things like this and never really have. I've never seen any compelling reason to spend a dollar on supplements like these and still don't ...

Hehe ... I hear you.

 

[MCsaxmaster]

Focusing away from photoautotrophs in natural reef systems towards heterotrophs and chemolithotrophs in marine aquaria ... what do you see as the reservoirs of vitamins that heterotrophic and chemolithotrophic bacteria are drawing upon (if any)?

I would have to say detritus. Some of this will be from leftover food, some from faeces and some from senescent algae and microbes.

Point well taken ... you see no potential for an accumulation of macro-aggregates immediately adjacent to a bacterial colony (whether autotrophic, or not) to do anything interesting (in terms of gradient formation --> ^ net uptake)?

Sure, I have no doubt little pieces of detritus and such get stuck in pores like that and decomposed. That's to be expected and happens no matter what we do or don't do.

Do you think that "pulsing" N or P through an aquarium's water column has the potential to generate a transient gradient which would temporarily increase net uptake?

Certainly. Diffusion has everything to do with concentration gradients. If the N and P in the water is increased the rate of diffusion through the diffusive boudary layer will increase and, if the organisms are N or P limited or N,P co-limited, increase gross production. Increased gross production doesn't imply increased net production or standing stock, however, as has been demonstrated several times with diverse groups of algae/microbes on reefs.

Chris

 

[mesocosm]

Chris ... apologies for not getting back to this sooner, but your posts have caused me to go "back to the basics" and do some serious pondering.

As a result of my pondering ... I stand corrected.

Measurement and prediction of mass transfer to experimental coral reef communities
M. E. Baird and M. J. Atkinson
Lirnnol. Oceanogr., 42(g), 1685-1693
1997

Abstract

The uptake of nutrients (N and P) into coral reef communities is proposed to be limited by diffusion through concentration-depleted boundary layers between the water and organisms, or what is termed “mass transfer limitation.” The mass transfer rate is a physical limit to the rate of nutrient uptake. Maximum uptake rates by highly rough biological surfaces have not yet been evaluated. Engineering correlations indicate that increased surface roughness should increase mass transfer, although it has been difficult to quantify roughness of living corals. In this paper, the effects of highly rough coral surfaces on mass transfer were investigated by using dissolution of gypsum (Plaster-of-Paris) from flat smooth surfaces and coral skeletons. The gypsum dissolution rates were measured as an increase in concentration of calcium ions in freshwater recirculating over experimental surfaces. Stanton numbers (St(m) a dimensionless number giving the ratio of uptake rate per unit area to the rate of advection of the substance past the uptake surface) of experimental smooth surfaces ranged from 2.6 to 3.5 X lo-’ and were the same as values in the engineering literature for smooth surfaces. St(m) for coral-shaped surfaces ranged from 70 X 10. ’ at 0.03 m s-l to 17 X 10 5 at velocities up to 0.50 m s-l and were in general 9 & 1 times that of smooth surfaces. The measured St(m) for each coral-shaped surface was the same as the predicted St(m) (+ 10%) calculated from measured friction and roughness using a correlation of heat transfer. St(m) for ammonia uptake on living coral reef communities show the same relationship between mass transfer, friction, and roughness as the coral-shaped gypsum surfaces. The transport rates of nutrients to reef surfaces are controlled by large-scale roughness, typically associated with coral heads, and not small-scale roughness elements on the organisms, nor biological alterations of diffusive boundary layers. Nutrient uptake and possibly other metabolic exchange rates are governed by concentration, water velocity, and friction dissipated over the reef, denoting that coral reef community metabolism is physically forced.

Full Article (pdf)
http://aslo.org/lo/toc/vol_42/issue_8/1685.pdf

For anyone who missed it ...

The transport rates of nutrients to reef surfaces are controlled by large-scale roughness, typically associated with coral heads, and not small-scale roughness elements on the organisms, nor biological alterations of diffusive boundary layers. Nutrient uptake and possibly other metabolic exchange rates are governed by concentration, water velocity, and friction dissipated over the reef, denoting that coral reef community metabolism is physically forced.

Time to lose my infatuation with diffusion across concentration-depleted boundary layers & biological alteration of boundary layers (which was really my whole point) as the determinant variables regulating nutrient uptake.

:thumbsup: :thumbsup:

 

[Fredfish]

First, thanks for putting more advanced back into the advanced forum. Talk about drinking from a firehose though...

A moment ago I dropped this in, "the bacteria are being detached and disrupted such that the bacterial community is no longer able to generate a microclimate that facilitates growth". Again, this implies that, in some situations, it's not the nutrients presented within the water column that matters most. I get that from this ...

Have either of you come across studies or papers postulating what advantage cyanobacteria gains by growing in sheets? I have often wondered if this is some sort of nutrient sequestering strategy ie: sheet over your nutrient source before something else grows to take advantage of it.

The cyanobacteria in my tank comes and goes. Sometimes it is in areas of flow, sometimes over part of the sand bed and sometimes it sheets over macro algaes that are dying back. There is no real consitancy in where it grows in my system.

Fred