"Biodiversity is dead, long live biodiversity" 10 month microbiome data from BRStv.

[GARRIGA]

Well chlorine naturally reacts with any organic material to form chloramines...not only ammonia

I'm being specific to that found in my tap and purposely placed there for human pathogen removal. Wasn't a thing in the 80s. Don't recall it in the 90s, either. At some point municipalities decided this was better. Obviously, a city thing. Well water doesn't have this although sulfur and farm run off do exists.

 

[livinlifeinBKK]

I know they aren't rubble. Thought because on egg crate it was being used in a sump.

Yeah, they get it and sell out so quickly they just set it in whatever tank is easiest to grab and bag it from.

 

[GARRIGA]

Yeah, they get it and sell out so quickly they just set it in whatever tank is easiest to grab and bag it from.

Got it. Thought this was your tank and not the vendor. We have similar option in Tampa. Source where I'd likely get my rubble from.

 

[livinlifeinBKK]

Btw, ammonia has been used in drinking water as a disinfectant for several decades i believe.

 

[TCseh]

I've meant to start this discussion thread for a while... so here we go.

Reef hobbyists have a lot of ideas about biodiversity and what it means in a reef system. A lot of these ideas (mine included) are reasoning from personal experience of myself and others, and how we think it ought to work. Mostly this is because the concepts are fuzzy and we just don't have much data - so reasoning from collective experience is the best we've got in these data-sparse areas.
But that's changing - there are a lot of concepts in this discussion that we now actually have pretty good data to ground ourselves in and think more concretely about - surrounding the concepts of biodiversity, maturity, balance etc. BRS did a series of 11 videos (full playlist) in 2022 "Biome Cycling" involving 12 side by side aquaria run in parallel for 10 months, with detailed observations and data. This was done at a scale and expense that the hobbyist can't duplicate and I think the results are of good quality, and the data is worth digesting even if I don't buy all his reasoning and conclusions. Given how much we think and talk about these ideas like the "ugly phase", biodiversity, maturity, balance etc - this data deserves way more discussion than it has received so far. It's a ton of data, observations, and reasoning to sift through. Way more than one post,
So I'll try to occasionally pull one big idea at a time that I think is well demonstrated by the data, and is worth talking about.

Short summary of the overall exercise. (meet the tanks - Ep 3)
They started 12 tanks from different initial ingredients:
1) Dry sand and Rock - control
2) Dry sand and Rock + Coral frags/colonies
3) Dry rock, live sand in a bag
4) Synthetic live rock cured in seawater
5) Dry Rock and sand + live rock rubble cured in the dark, in dark sump
6) Live Rock and Sand directly from established tank
7) Dry rockand sand + 2 cups of established tank sand
8) Paper-wet indonesian live rock and dry sand
9) Gulf live rock shipped in water and dry sand
10) Dry rock and sand + Aquaforest reef mud
11) Dry rock and sand + 100% water from established system
12) Dry rock and sand + biobrick from established system

All tanks were given two clownfish and were kept dark for 4 weeks, then moderate "LPS lighting" from weeks 5-10, then high "SPS lighting" from weeks 11-15.
They tested each tank via aquabiomics at week 2, week 4, 10, and 15.
(What aquabiomics is and what was measured - Ep 4)


Idea 1: Biodiversity is dead, Balance is the new "biodiversity"
Aquabiomics gives two overall statistical measures/scores:
Biodiversity is a statistical measure of the bacterial families that make up more than 1% of the measured genetic material.
Balance is a measure of how much the present bacterial families look similar to those in established reef systems.

Here's the backwards thing that kills many ideas about biodiversity (like mine). In essentially every system that was started with any live material, The Biodiversity fell while the Balance rose. The biodiversity is initially higher especially in tanks started with a lot of live material like the live rock, but gradually falls. The Balance score - on the other hand, starts extremely low, but in every decent-looking tank climbs over time to more closely resemble typical reef tanks.
So early on, the high biodiversity likely represents a disturbed system, with many food sources of dead, disturbed and out of place organisms, and quick bacterial growth in response - but those early bacterial families look nothing like the eventual expected families that will make up a well-established tank.
Put another way, it is the death and loss of early bacterial diversity that helps shape the microbiome to look more like eventual reef systems. The Balance is a far better measure of this process of moving towards an established system than the biodiversity is, and perhaps the balance score isn't a terrible marker for biofilm maturity and system stability overall.
Ryan explains this idea of high biodiversity in tanks that look awful, and the balance being a better indicator here Ep 7 3:01-3:48

This data is in the videos Ep 5, 6, 7.









And here's Idea 2a and 2b in post 51 - all the biodiversity numbers followed the same trend of a drop and then rise during the 15 weeks, but the balance scores went different directions - likely more reflective of different progression of the tanks.

Idea 3 in post 73 - 50th percentile diversity was really hard to acheive, only 1 tank got there. But most tanks got to 50th percentile balance, and some quickly.

here's a rundown of what aquabiomics has measured or concluded about many Frequently Asked Questions regarding hobby tank microbiomes in post 101

Idea 4 in post 110 - Not every bacteria you add actually becomes part of the community in the system, even major bacterial families sometimes don't transfer over.

Idea 5a in post 129 - every BRS test tank had the same uncommon family as a major part of the system during the 15 weeks. Not totally clear why.

Idea 5b in post 157 - aquabiomics did mutliple tests with adding material to new or established systems that superficially looked similar to BRS tests - but resulted in far far more diverse results in a much shorter time frame. Maybe live rock and sand can be dramatically different in the microbiome they seed.

Idea 6 in post 227 - There were groups of tanks that converged to similar results by the 10 and 15 week tests. This is seen hobby-wide, many tanks converge to similar long-term communities. But not all tanks do - some converge to a different community and some of the BRS tank communities didn't look like any of the others at 10-15 weeks.
Additionally - 5 tanks that looked near-identical in community at week 10, went totally different directions by week 15. Maturation of a bacterial community is likely a very slow process and there were still effects pushing tanks in different directions between weeks 10-15.

My attempt at some sort of conclusions in post 229 - microbial stability takes a long time, can be lost when the tank does through big disruptions and can be restored over time.

With BRS becoming more focused in marketing instead of aquarium health. I still decided to do the copepods + af life source they recommend in these videos.

My tank has been running for over 6 months. I have kept nitrates over 15 and at the highest in the 50s. I have added coral with small amounts of algae, so it is in my tank. I haven't had anything worse than some film algae that you wouldn't even notice 90% of the time and it disappears a day or two later. I haven't had any fish in the tank for the last two months due to Wipeout, meaning I don't have 100 tangs eating it all up. I only have a couple snails and hermits.

I have a 50g long tank. 30g sump. I dosed 4 bottles of galaxy pods from algae barn.

I highly suggest others to try and come up with an opinion for themselves rather than judging brs as a company.

 

[livinlifeinBKK]

With BRS becoming more focused in marketing instead of aquarium health. I still decided to do the copepods + af life source they recommend in these videos.

My tank has been running for over 6 months. I have kept nitrates over 15 and at the highest in the 50s. I have added coral with small amounts of algae, so it is in my tank. I haven't had anything worse than some film algae that you wouldn't even notice 90% of the time and it disappears a day or two later. I haven't had any fish in the tank for the last two months due to Wipeout, meaning I don't have 100 tangs eating it all up. I only have a couple snails and hermits.

I have a 50g long tank. 30g sump. I dosed 4 bottles of galaxy pods from algae barn.

I highly suggest others to try and come up with an opinion for themselves rather than judging brs as a company.

I don't think of them as anything more than another supplier...i personally wouldn't listen to anyone who's trying to sell something make claims about how great their product is.

 

[TCseh]

I don't think of them as anything more than another supplier...i personally wouldn't listen to anyone who's trying to sell something make claims about how great their product is.

I agree. With you seeing them as a supplier, I am just another hobbyist, so if you don't believe what they tell you. Believe what I tell you.

 

[livinlifeinBKK]

I agree. With you seeing them as a supplier, I am just another hobbyist, so if you don't believe what they tell you. Believe what I tell you.

Im Not Sure if you're being sarcastic or funny.

 

[taricha]

That's another thing I've always been skeptical about...it doesn't seem adding a few grams of crushed up rock would do much if anything in regards to populating a large or even medium sized tank. Also they live on surfaces so I'd doubt throwing them in a reactor is really going to be very effective overall...i think your idea is to scatter the bacteria all over the tank but if a few bacteria are surrounded by hundreds of others, I don't think they'll make it too long unless there's something very special about that particular bacteria

This is a good question that gets confusing.
We know that if we are transferring rock, we are seeding biofilm. We know that biofilm bacteria are mostly in the film and not much in the water, so we jump to - doesn't spread by water. That last leap isn't true. Everything is a little bit in both, and can be measured in both.
@Dan_P has done the same thing with nitrifiers. Measured a constant release of active nitrifiers into the water from an established biofilm grown from biospira.

Below is a clip of Eli talking about this water/film distinction that's never really absolute...

Q7 Are some bacteria only in water, and others only on surfaces?
LinkQ7
Although some groups grow on surfaces, they are easily measured in the water. Likewise groups that live in the water are measured on surfaces. These distinctions aren’t absolutes, and the same applies to nitrifiers.

Biofilm bacteria are constantly releasing cells to spread and go elsewhere - And if you place rock into an overflow then you are putting a lot of flow across the surfaces to facilitate these biofilm species to spread everywhere. The rate of succession/maturation on the new raw surfaces you want colonized will be agonizingly slow - but it will occur.

Here's some example data to back the notion of live sand actually significantly increasing the measured diversity in tanks that were established.

I wanted to see if there were examples of other people replicating aquabiomics results, and I found two that actually did before/after with added live material.
example 1
before : number = 300 , percentile = 36
after Live sand from IPSF: number = 488 , percentile = 86

example 2
before: number = 162, percentile = 05
after live sand also from IPSF: number = 726, percentile = 99

In other words, it looks like the aquabiomics results and not at all like the BRS ones.

so the answer to this question is probably yes, aquabiomics results were repeatable....

Full thing is here in post 201

 

[livinlifeinBKK]

This is a good question that gets confusing.
We know that if we are transferring rock, we are seeding biofilm. We know that biofilm bacteria are mostly in the film and not much in the water, so we jump to - doesn't spread by water. That last leap isn't true. Everything is a little bit in both, and can be measured in both.
@Dan_P has done the same thing with nitrifiers. Measured a constant release of active nitrifiers into the water from an established biofilm grown from biospira.

Below is a clip of Eli talking about this water/film distinction that's never really absolute...


Biofilm bacteria are constantly releasing cells to spread and go elsewhere - And if you place rock into an overflow then you are putting a lot of flow across the surfaces to facilitate these biofilm species to spread everywhere. The rate of succession/maturation on the new raw surfaces you want colonized will be agonizingly slow - but it will occur.

Here's some example data to back the notion of live sand actually significantly increasing the measured diversity in tanks that were established.



Full thing is here in post 201

I actually heard that talk! That's why I commented this afterwards:

If they're on rubble then a majority of them will not be free swimming. You're correct that some will be scattered and dispersed through the aquarium, but again, if they naturally form biofilms they are going to be very vulnerable to competition initially. Also, the environment conditions both biotic and abiotic affect settlement and how easily they'll form their biofilm. Some actually can migrate on their own. This is why I don't see a few grams of gravel being very effective. I certainly wouldn't expect them to multiply very quickly on new surfaces either although that depends on the species.

 

[Dan_P]

This is a good question that gets confusing.
We know that if we are transferring rock, we are seeding biofilm. We know that biofilm bacteria are mostly in the film and not much in the water, so we jump to - doesn't spread by water. That last leap isn't true. Everything is a little bit in both, and can be measured in both.
@Dan_P has done the same thing with nitrifiers. Measured a constant release of active nitrifiers into the water from an established biofilm grown from biospira.

Below is a clip of Eli talking about this water/film distinction that's never really absolute...


Biofilm bacteria are constantly releasing cells to spread and go elsewhere - And if you place rock into an overflow then you are putting a lot of flow across the surfaces to facilitate these biofilm species to spread everywhere. The rate of succession/maturation on the new raw surfaces you want colonized will be agonizingly slow - but it will occur.

Here's some example data to back the notion of live sand actually significantly increasing the measured diversity in tanks that were established.



Full thing is here in post 201

A biofilm represents limited real estate. There is limited surface area to spread in 2-D and the thickness is limited by diffusion rate. An actively growing biofilm has to disperse at some point. Quorum sensing lets the biofilm know when to migrate. I view aquarium surfaces as upside down rain clouds raining bacteria (virus, fungi, algae, etc) upwards. Dipping a microscope slide in your aquarium for a few days to weeks will give you a glimpse of the rain.

 

[brandon429]

really well said. in tuffloud's connected tank experiment he cycled a completely dry rock and dry sand system in 20 days of only inputting reef water from another running reef tank, no extra feed specific for the new tank and no bottle bac at all. he at least had his cycle completed within the timeframes of the common cycling chart/free o charge which I thought was great. cycling bac 100% can be transmitted in water we discerned. this always left me pause as to why Dr Tim in the well-known youtube macna video on cycling said reef water doesn't contain cycling bacteria, it contains enough to at least comply with a cycling chart timing.

 

[GARRIGA]

really well said. in tuffloud's connected tank experiment he cycled a completely dry rock and dry sand system in 20 days of only inputting reef water from another running reef tank, no extra feed specific for the new tank and no bottle bac at all. he at least had his cycle completed within the timeframes of the common cycling chart/free o charge which I thought was great. cycling bac 100% can be transmitted in water we discerned. this always left me pause as to why Dr Tim in the well-known youtube macna video on cycling said reef water doesn't contain cycling bacteria, it contains enough to at least comply with a cycling chart timing.

Could be related to the point he makes about establishing autrophs first and perhaps tank water containing heterotrophs might impede that progress or just salesmanship to support buying a bottle which contains bacteria in water.

 

[Dan_P]

really well said. in tuffloud's connected tank experiment he cycled a completely dry rock and dry sand system in 20 days of only inputting reef water from another running reef tank, no extra feed specific for the new tank and no bottle bac at all. he at least had his cycle completed within the timeframes of the common cycling chart/free o charge which I thought was great. cycling bac 100% can be transmitted in water we discerned. this always left me pause as to why Dr Tim in the well-known youtube macna video on cycling said reef water doesn't contain cycling bacteria, it contains enough to at least comply with a cycling chart timing.

The guy has to make a buck…

I have “cycling” an aquarium with aquarium water on my to do list.

 

[Nano sapiens]

A few of my thoughts on this...

Consider this: In a drop (one millilitre) of seawater, one can find approximately 10 million viruses, one million bacteria and about 1,000 small protozoans and algae

I have always found it amusing when I see statements like, "There are no substrate living microbes in the water column"...and visa-vesa. If you have a water environment, you will have all the microbes that are in the system present everywhere, just in often vastly different proportions/concentrations.

When a microbe is present in a fully functional ecosystem and it is the best adapted to a specific micro-environment, then it will become the dominant species in that particular micro-environment. However, since there are micro-environments within micro-environments, within micro-environments, etc., the idea that one species can completely eliminate another system wide is just not possible (unless an introduced microbe can't physically survive in a particular medium). When the environment shifts (think 'dynamic equilibrium'), sub-dominant species can quickly become the dominant ones and this is a perpetual on-going process in our systems. And this is why a system can be so amazingly resilient. However, there are limits, and if conditions alter too drastically then transitions to an alternate state (ex.: coral dominated reef transforming into an alga/microbe one) are inevitable.

 

[brandon429]

I ventured to think the statement may have originated from the inherent biology that cycling bacteria may not detach then swim through the water in the classic style

but the shear rates are high in our systems by design, and castings are part and parcel of a reef tank. anyone on this site can take a 3 pound representative of their best live rock sample, and clean it externally very well in saltwater, as clean as you want to make it. rinse it 1500 times for example, that's dang clean.

then set that live rock in a white paint bucket temp reef with a common powerhead and let the rock exist 48 hours in a mini shear envion: on the third day (or maybe within the 3rd hour) there will be detritus castings lining the bottom of the bucket clearly visible

=rafts that carry and distribute the necessary players for ammonia control, all suspended and whirling around at the rates Ralph mentions above

whatever has the inherent surface slicks containing our bac are being fragmented and sent around constantly without fail in all reef systems

those bac may not be free-swimming but they're white water rafting for darn sure, little pilgrims

 

[Nano sapiens]

those bac may not be free-swimming but they're white water rafting for darn sure, little pilgrims

Absolutely. Something as innocuous as the swish of a fish's tail against the back wall can dislodge tens-of-thousands of biofilm microbes that go 'white water rafting' (and just think what a tank cleaning can do!).

On a microbial level, every living system is constantly resetting itself no matter how hard we try to keep things 'perfectly stable'. Good thing we can't actually see this happening or we might develop RNBS ('Reefer Nervous Breakdown Syndrome')

 

[GARRIGA]

How does UV filtration then affect diversity?

 

[Nano sapiens]

How does UV filtration then affect diversity?

Effective UV substantially reduces water-column borne microorganisms such as Pelagibacteraceae which make up a substantial portion of the 'normal' reef microbiome (as defined by AquaBiomics data set). Since many reef systems run fine with UV in varying degrees, loosing the bulk of certain species apparently is not such a big deal as other UV unaffected substrate living microbes can fill in (microbes tend to be very adaptable and have multiple energy acquisition modes, so they can 'fill in for each other', so to speak). Pelagibacteraceae is consumed by at least some coral species (mucus netting), but I'm not sure as to the percentage of their total nutrient uptake.

 

[Reef Psychology]

Wow, there is a lot going on with this thread. I am not a reef expert, but I am a scientist. BRS does a pretty good job with information, but not really with science. In the last 5 years the entire hobby has changed and BRS has reported on this. I respect their informational efforts. I have learned from them. I respect the capitalistic endeavor. I do not LIVE UNDER capitalism, I thrive in it, and I am glad that BRS does too. It is a good thing.

The fact is that there are way too many variables in a bazillion different systems of application to really have any kind of scientific approach to the "biodiversity" question in the aquarium industry. AKA, your milage may vary.

And by the way, bazillion is not a scientific term...

Yeah, well said. I’m in behavioral science and BRS leaves a lot to be desired. Their biggest issue, I think, is the overly broad aspect of their approach. However, it would very boring for the lay person to sit and watch well constructed scientific research.

Gotta entertain them as well as inform. It may be anecdotal, but it’s still something more than we had last year - so that’s something.