School Project for Reef Biological Filtration

Reef-Explorer

New member
Hello all, I am doing a school project for grade 10. The project is based on designing a marine reef tank filtration system with the main focus on biological filtration (microbes).
I have a basic awareness of the carbon cycle and nitrogen cycle.
However, I would love to do some reading on the identification and function of bacteria/microbes in the filtration system.
  • Can you please propose a list of literature and books for my level?
  • I would also like to have literature that gives a basic understanding of the microbes and how they relate to the ecosystem and the impact of climate change on these microbes.
Thank you in advance
 
Since my focus has shifted from "nutrients" to DOC (Dissolved Organic Carbon) and microbial processes I'm of the opinion anything that disrupts the or prevents maintaining healthy microbiomes is contraindicatred. So yes, this applies to any coral kept in aquaria. Here's two mixed reefs systems I've maintained without skimmers:

90 Gallon Mixed Reef Maintained with Tapwater

500 gallon

Here's some more links you may find informative:

"Coral Reefs in the Microbial Seas " This video compliments Rohwer's book of the same title. Used copies are available on line and it may be free to read on Internet Archive. both deal with the conflicting roles of the different types of DOC (carbon dosing) in reef ecosystems and how it can alter coral microbiomes. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems and are an excellent starting point to understand the conflicting roles of Dissolved Organic Carbon (DOC, aka "carbon dosing") in reef ecosystems.

Delbeek Molar Ratios

Changing Seas - Mysterious Microbes

Microbial view of Coral Decline
- YouTube

Nitrogen cycling in hte coral holobiont
- YouTube

BActeria and Sponges
- YouTube

Maintenance of Coral Reef Health (refferences at the end)
- YouTube

Optical Feedback Loop in Colorful Coral Bleaching
- YouTube

DNA Sequencing and the Reef Tank Microbiome
- YouTube

Richard Ross What's up with phosphate"
- YouTube

This may help some. I’ll also tag the poster @Timfish as he’s very knowledgeable with this
 
Hello all, I am doing a school project for grade 10. The project is based on designing a marine reef tank filtration system with the main focus on biological filtration (microbes).
I have a basic awareness of the carbon cycle and nitrogen cycle.
However, I would love to do some reading on the identification and function of bacteria/microbes in the filtration system.
  • Can you please propose a list of literature and books for my level?
  • I would also like to have literature that gives a basic understanding of the microbes and how they relate to the ecosystem and the impact of climate change on these microbes.
Thank you in advance

The best book I've come across foe explaining in layman's terms some of the microbial stuff is Forest Rohwer's "Coral Reefs in the Microbial Seas". Last I looked it is out of print but one idea is you might try contacting him and see if you can get a .pdf copy to share with your students. You might be able get it on archive.org also: Coral reefs in the microbial seas : Rohwer, Forest : Free Download, Borrow, and Streaming : Internet Archive

Here's a list of links I've collected as well. An important aspect of the dissolved organic carbon carbon cycle is the role sponges play in recycling the DOC released by corals and algae. Unfortunatly I have not found any publication that incorporates the work on DOC with corals and algae with DOC and sponges.


Videos:

"Coral Reefs in the Microbial Seas " This video compliments Rohwer's book of the same title. Used copies are available on line and it may be free to read on Internet Archive. Both deal with the conflicting roles of the different types of DOC (carbon dosing) in reef ecosystems and how it can alter coral microbiomes. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems and are an excellent starting point to understand the conflicting roles of Dissolved Organic Carbon (DOC, aka "carbon dosing") in reef ecosystems.

Delbeek Molar Ratios

Changing Seas - Mysterious Microbes

Microbial view of Coral Decline

Nitrogen cycling in hte coral holobiont

BActeria and Sponges
- YouTube

Maintenance of Coral Reef Health (refferences at the end)
- YouTube

Optical Feedback Loop in Colorful Coral Bleaching
- YouTube

DNA Sequencing and the Reef Tank Microbiome
https://www.youtube.com/watch?v=ghxVSmLhxUg

Richard Ross What's up with phosphate"
https://youtu.be/ZRIKW-9d2xI

 
Looks like my first ppost was too wordy :D

Here's more links:

Algae and DOC:

FYI: DOC can be roughly seperated into three catagories, Labile, Semirefractory and Refractory. Most of the following papaers are looking mainly at Labile DOC. This will raise the hackles on some reefers but keep in mind Labile DOC and Carbon Dosing are synonamous. Jasper deGeoij's work shows cryptic sponges remove labile DOC about a thousand times faster than bacterioplankton. Included are links to some of the research showing what cryptic sponges are doing as well. Also, researchers tend to use DOM (Dissolved Organic Matter) and DOC (Dissolved Organic Carbon) interchangebly.

long-term stony coral survival in the Coral Reef Exhibit at Reef HQ Aquarium, Townsville, Australia with an ATS was measured in days, not years. (See figure 3) (This page may have been removed, I can send you a copy of the .PDF if you're interested)

Indirect effects of algae on coral: algae‐mediated, microbe‐induced coral mortality

Influence of coral and algal exudates on microbially mediated reef metabolism.
Coral DOC improves oxygen (autotrophy), algae DOC reduces oxygen (heterotrophy).

Role of elevated organic carbon levels and microbial activity in coral mortality

Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity
Algae releases significantly more DOC into the water than coral.

Pathologies and mortality rates caused by organic carbon and nutrient stressors in three Caribbean coral species.
DOC caused coral death but not high nitrates, phosphates or ammonium.

Visualization of oxygen distribution patterns caused by coral and algae

Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates
Exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria.

Microbial ecology: Algae feed a shift on coral reefs

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

Elevated ammonium delays the impairment of the coral-dinoflagellate symbiosis during labile carbon pollution
(here's an argument for maintaining heavy fish loads if you're carbon dosing)

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton

Unseen players shape benthic competition on coral reefs.

Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.

Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

Macroalgal extracts induce bacterial assemblage shifts and sublethal tissue stress in Caribbean corals.

Biophysical and physiological processes causing oxygen loss from coral reefs.

Global microbialization of coral reefs
DDAM Proven

Coral Reef Microorganisms in a Changing Climate, Fig 3

Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes


Sponges and DOC

Element cycling on tropical coral reefs.
This is Jasper de Geoij's ground breaking research on reef sponge finding some species process labile DOC 1000X faster than bacterioplankton. (The introduction is in Dutch but the content is in English.)

Sponge symbionts and the marine P cycle

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Differential recycling of coral and algal dissolved organic matter via the sponge loop.
Sponges treat DOC from algae differently than DOC from corals

A Vicious Circle? Altered Carbon and Nutrient Cycling May Explain the Low Resilience of Caribbean Coral Reefs

Surviving in a Marine Desert The Sponge Loop Retains Resources Within Coral Reefs
Dissolved organic carbon and nitrogen are quickly processed by sponges and released back into the reef food web in hours as carbon and nitrogen rich detritus.

Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)

The Role of Marine Sponges in Carbon and Nitrogen Cycles of COral Reefs and Nearshore Environments.

Microbially mediated nutrient cycles in marine sponges
 
Hello again,
I have a couple of questions.

1. I know the carbon and nitrogen cycles and their functions. But what are some other major cycles that apply in the marine filtration system?
2. What is the role of phosphate in the marine filtration system? The nitrogen and carbon cycles don't use phosphate yet every video I watch includes phosphate somewhere.
 
Hello again,
I have a couple of questions.

1. I know the carbon and nitrogen cycles and their functions. But what are some other major cycles that apply in the marine filtration system?
2. What is the role of phosphate in the marine filtration system? The nitrogen and carbon cycles don't use phosphate yet every video I watch includes phosphate somewhere.
An excess of phosphates can lead to nuisance algae issues. You want to shoot for 0.01-0.03 ppm. I’ve also, anecdotally, found that an imbalance between PO4 and NO3 can lead to Cyanobacteria outbreaks. NO3 should be in the 1-10 ppm.
 
Hello again,
I have a couple of questions.

1. I know the carbon and nitrogen cycles and their functions. But what are some other major cycles that apply in the marine filtration system?
2. What is the role of phosphate in the marine filtration system? The nitrogen and carbon cycles don't use phosphate yet every video I watch includes phosphate somewhere.
So this question was also about the actual chemical formula where phosphate would appear and how microbes would participate in this regard.
So please share those details if you can.

Also please list out any other major chemical processes I need to focus on other than Nitrogen and Carbon cycles.
 
So this question was also about the actual chemical formula where phosphate would appear and how microbes would participate in this regard.
So please share those details if you can.

Also please list out any other major chemical processes I need to focus on other than Nitrogen and Carbon cycles.
Phosphate in the Reef Aquarium
11.jpg
The “simplest” form of phosphorus in seawater is inorganic orthophosphate (sometimes called Pi by biologists). It consists of a central phosphorus atom surrounded by four oxygen atoms in a tetrahedron

http://reefkeeping.com/issues/2004-10/rhf/index.php
http://reefkeeping.com/issues/author/rhf.php
https://reefs.com/author/randy-holmes-farley/

That should keep you busy for a while.


and now the simplistic answer that is actually the core of the issue. We place food in the tank. Animals digest it like a fish. What comes out of the fish may be redigested by a crab and then a snail and eventually microbes.

Foods are nearly always the primary source of phosphate in reef aquaria, and rarely does a reefer need to look further when tracking down a phosphate problem. A quote from the first article.

We look at food as a top of the food chain organism. A bottom of the food chain organism searches for a steady supply of some particular type of chemical bonds it can break and derive energy from.

The metabolic breakdown scheme for typical organic materials in phytoplankton1 is shown below:
1761501991331.png

organic + oxygen → carbon dioxide + water + hydrogen ion + phosphate + nitrate
https://www.reef2reef.com/ams/phosphate-in-the-reef-aquarium.9/
https://www.reef2reef.com/ams/authors/randy-holmes-farley.45227/

Randy writes fairly easy to understand articles on most reef chemistry things. As you can see his stuff is spread all over the place.
 
Last edited:
Hello again,
I have a couple of questions.

1. I know the carbon and nitrogen cycles and their functions. But what are some other major cycles that apply in the marine filtration system?
2. What is the role of phosphate in the marine filtration system? The nitrogen and carbon cycles don't use phosphate yet every video I watch includes phosphate somewhere.

As can be seen in the article on the Redfield ratio linked to above, phosphorus is an essential component when talking about any living organisms and carbon and nitrogen. A oint that seems t be missed, since phosphorus is the lowest number in the canonical ratio, it is the easiest to reduce and create a shortage

Unfortunately, aquarists often focus on just Dissolved Inorganic Phosphorus (DIP, aka PO4, phosphate, orthophosphate) when the food webs in our aquaria (and any ecosystem for that matter) include Dissolved Organic Phosphorus (DOP) anf Particulate Organic Phosphorus (POP). Unfortunately, testing for the organic forms is not something most aqauarists can do.

It's important to understand with both carbon and nitrogen we have the same problem. We are only able to test for the dissolved inorganic forms. We cannot easily quantify the dissolved organic forms or the particulate organic forms. This causes problems when trying to use the Redfield ratio on our aquaria as we are not able to quantify all the forms of carbon, nitrogen and phosphorus.

As the microbial processes are critical in our aquaria (and all more complex life forms) it's important to keep the points Charles Delbeek is making, in his video posted above, in perspective. The ratio he's promoting is closer to what's found in microbes in the water, not necessarily the ratio found in corals or other organisms.

To take a closer look at the phosphorus cycle in corals, this paper looks how the three basic forms, DIP, DOP and POP, can be both taken up by corals for thier needs and released as excess phosphorus. So, as pointed out above, while food is by and far the primary source for phosphorus being introduced into aquaria, depending on what and how corals are feeding influenes what forms they are excreting. So it's possible corals themselves are the primary source of phosphate. Here's Fig. 3 from teh paper on phosphorus metabolism linked to.
DIP DOP POP.jpg

On a final note, it is important to understand serious problems can be caused for corals by keeping phosphate or PO4 below .03 mg/l. Depending on the forms of the available phosphorus, some aquarist are able to keep corals with PO4 below .03 mg/l but without being able to test for organic forms this is shooting in the dark. Unfortunately, this became a wide spread reccomendation by a few based on faulty assumptions and inadequate research. J. E. N. Veron's observation* published in 1994, that corals on nutrient poor reefs are not as lush and that upwelling provides .3 mg/l should have raised questions about keeping inorganic levels low. Szmant (2002) pointed out research used to justify low levels had serios flaws. More recently, research done at Southampton University in England (1) (2) (3) (4) diffinitevly showed PO4 levels needed to be kept above .03 mg/l to prevent phosphate deficencies in corals.


*"Imported nutrients are usually transported to reefs from rivers; but if there are no rivers, as with reefs remote from land masses, nutrients can only come from surface ocean circulation. Often this supply is poor, and thus the vast ocean expanses have been refered to as "nutrient deserts". The Indo-Pacific has many huge atolls in these supposed deserts which testify to the resilience of reefs, but the corals themselves may lack the lush appearance of those of more fertile waters. Many reefs have another major supply of inorganic nutrients as, under certain conditions, surface currents moving against a reef face may cause deep ocean water to be drawn to the surface. This "upwelled" water is often rich in phosphorus (.3 mg/l) and other essential chemicals." J. E. N. Veron "Corals of Austrailia and the Indo-Pacific" pg 30


Here's some moe links on phosphorus:

Effects of phosphate on growth and skeletal density in the scleractinian coral Acropora muricata: A controlled experimental approach

High phosphate uptake requirements of the scleractinian coral Stylophora pistillata

Phosphorus metabolism of reef organisms with algal symbionts

 
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