Peer Review database in the hobby?

[Pankney72]

Hey all. I’m a guy with a science (biochemist/cell biologist) background and I’ve been reefing with a pretty minimalist system for quite a while now. That said, I’ve finally got the resources to do a custom build 250 gal before I move for work, and my question is this.

I’m sure peer reviewed stuff for our hobby is out there. @Humblefish , @randyBRS , and @Randy Holmes-Farley mention studies in their advice but I don’t usually see the references.

Where do you guys get your science from? Any good newer books out there like The Conscientious Marine Aquarist? I want to add bells and whistles to my new tank but I want to make sure they will add QOL to my system. Thanks a ton!

(by the by minimalist is my moderately stocked 125 mixed reef with good LEDs, skimmer, filter pads and religious water changes.)

 

[N.Sreefer]

Personally I just skim the studies on google scholar some great studies on chemistry in reef aquaria and trace elements in salt water. I find every book I see is outdated on taxonomy and modern lighting, filtration, and sources for livestock. If you have research credentials at work/school you can normally access the studies for free through your institution.

 

[NoahLikesFish]

i learn from experience and i use basically the same method you would in the 90s/2000s except i dose seachem & i run leds. no skimmer, filtration, water changes, just biofilter and flow can work miracles.

 

[NoahLikesFish]

i read on some stuff concerning like fish biology and reef biology and stuff but i just keep it simple and it works well. walstad's book on the planted aquarium is good for learning what makes algae tick & paul b's book does a good job talking about diy & its funny.

 

[Pankney72]

Personally I just skim the studies on google scholar some great studies on chemistry in reef aquaria and trace elements in salt water. I find every book I see is outdated on taxonomy and modern lighting, filtration, and sources for livestock. If you have research credentials at work/school you can normally access the studies for free through your institution.

That’s what I typically do, and I do have the access through my employer. Google scholar kicks the teeth in on other search engines haha. To be honest I posted this because I was looking at UV sterilizers for ich management but I couldn’t find a paper with information that would be transferable to a home system.

 

[jcolliii]

GS is pretty good, but if you have a large local university nearby, the databases that are paid for by some university systems will directly link a TON of full text stuff that GS won't. You can also sign up for an account on Research Gate - lots of folks share their work on that site. Also, if you find an article on GS that you want or need, email the lead or second authors - they usually have a pdf that they can share.

 

[flagg37]

You’ve got all the peers needed to review your stuff right here. :)

 

[Pankney72]

GS is pretty good, but if you have a large local university nearby, the databases that are paid for by some university systems will directly link a TON of full text stuff that GS won't. You can also sign up for an account on Research Gate - lots of folks share their work on that site. Also, if you find an article on GS that you want or need, email the lead or second authors - they usually have a pdf that they can share.

I use Google scholar to find what I need, then swap over to our systems for full text. Thank you for the quick response!

 

[NeonRabbit221B]

@Lasse often gives references to nitrite studies and may be able to help there.

 

[J1a]

That’s what I typically do, and I do have the access through my employer. Google scholar kicks the teeth in on other search engines haha. To be honest I posted this because I was looking at UV sterilizers for ich management but I couldn’t find a paper with information that would be transferable to a home system.

Try searching under mariculture journals. They have much more funding than reefing.

Imo the biggest hurdle to us hobbyist is not the lack of research (there are plenty) the issue is that hobbyist equipment is less transparent.

For instance, we know from some literature that ich can be reliably killed with exposure to UV radiation above 300000 uws/cm2. However there is no way for us to know, or measure that a given hobbyist equipment produce such irradiation.

 

[fish farmer]

Try searching under mariculture journals. They have much more funding than reefing.

Imo the biggest hurdle to us hobbyist is not the lack of research (there are plenty) the issue is that hobbyist equipment is less transparent.

For instance, we know from some literature that ich can be reliably killed with exposure to UV radiation above 300000 uws/cm2. However there is no way for us to know, or measure that a given hobbyist equipment produce such irradiation.

I was going to say the same thing aquaculture\mariculture, using the same equipment just on a bigger scale.

 

[N.Sreefer]

I would say recirculating aquaculture but not mariculture or flow through aquaculture. We don't have the advantage of exchange with the ocean.

 

[Pankney72]

Try searching under mariculture journals. They have much more funding than reefing.

Imo the biggest hurdle to us hobbyist is not the lack of research (there are plenty) the issue is that hobbyist equipment is less transparent.

For instance, we know from some literature that ich can be reliably killed with exposure to UV radiation above 300000 uws/cm2. However there is no way for us to know, or measure that a given hobbyist equipment produce such irradiation.

Exactly! I’m a bit of a purist in translating research into something applicable on my scale. Knowing that a battery that produces the UV fury of a thousand suns kills ich or some other industrial/commercial grade equipment equivalent doesn’t necessarily help me make purchase decisions for a 250 gallon home tank

 

[fish farmer]

This company sells various sized units commercial and smaller, they used to have data sheets, but I noticed the pages weren't found.
The company used to be Aquatic Ecosystems, https://pentairaes.com/. I know they used to do local display type installations in Florida so they were knowledgeable in smaller scale operations.

 

[Timfish]

Google scholar has been very helpful for me and you'll see me posting refferneces alot. There are some good videos on youtube (and lots of not so good ones). Here's some links I have bookmakred if you're interested:


"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title (Paper back is ~$20, Kindle is ~$10), both deal with the conflicting roles of the different types of DOC in reef ecosystems. 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


Changing Seas - Mysterious Microbes


Nitrogen cycling in hte coral holobiont


BActeria and Sponges


Maintenance of Coral Reef Health (refferences at the end)


Optical Feedback Loop in Colorful Coral Bleaching


Richard Ross What's up with phosphate"


Indirect effects of algae on coral: algae‐mediated, microbe‐induced coral mortality
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2006.00937.x
Influence of coral and algal exudates on microbially mediated reef metabolism.
Coral DOC improves oxygen (autotrophy), algae DOC reduces oxygen (heterotrophy).
https://peerj.com/articles/108/?utm_source=TrendMD&utm_campaign=PeerJ_TrendMD_0&utm_medium=TrendMD
Role of elevated organic carbon levels and microbial activity in coral mortality
http://www.int-res.com/articles/meps2006/314/m314p119.pdf
Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity
Algae releases significantly more DOC into the water than coral.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027973
Pathologies and mortality rates caused by organic carbon and nutrient stressors in three Caribbean coral species.
Starch and sugars (doc) caused coral death but not high nitrates, phosphates or ammonium.
http://www.int-res.com/articles/meps2005/294/m294p173.pdf
Visualization of oxygen distribution patterns caused by coral and algae
https://peerj.com/articles/106/
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719127/
Microbial ecology: Algae feed a shift on coral reefs
https://www.nature.com/articles/nmicrobiol201661
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.
https://www.ncbi.nlm.nih.gov/pubmed/23303369
Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching
https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.13695
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)
https://www.sciencedirect.com/science/article/pii/S0166445X19307192
Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton
https://www.nature.com/articles/ismej2017142
Unseen players shape benthic competition on coral reefs.
https://www.ncbi.nlm.nih.gov/pubmed/22944243
Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.
https://www.ncbi.nlm.nih.gov/pubmed/27795310
Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.
https://www.ncbi.nlm.nih.gov/pubmed/22957055
Macroalgal extracts induce bacterial assemblage shifts and sublethal tissue stress in Caribbean corals.
https://www.ncbi.nlm.nih.gov/pubmed/23028648
Biophysical and physiological processes causing oxygen loss from coral reefs.
https://elifesciences.org/articles/49114.pdf
Global microbialization of coral reefs
DDAM Proven
https://www.nature.com/articles/nmicrobiol201642
Coral Reef Microorganisms in a Changing Climate, Fig 3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7096749/figure/fig3/
Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes
https://msystems.asm.org/content/msys/3/2/e00162-17.full.pdf

Because sponges are essential players in the carbon, nitrogen and phosphorus cycle(s) on reefs here's some links to research done with them.

Element cycling on tropical coral reefs.
This is Jasper de Geoij's ground breaking research on reef sponges. (The introduction is in Dutch but the content is in English.)
https://www.rug.nl/research/portal/files/14555035/13completethesis.pdf
Sponge symbionts and the marine P cycle
https://www.pnas.org/content/112/14/4191
Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges
https://www.pnas.org/content/112/14/4381
Differential recycling of coral and algal dissolved organic matter via the sponge loop.
Sponges treat DOC from algae differently than DOC from corals
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.12758
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.
https://www.researchgate.net/publication/279061640_2013_deGoeij_Science_Sponge_loop
Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934968/
The Role of Marine Sponges in Carbon and Nitrogen Cycles of COral Reefs and Nearshore Environments.
https://search.proquest.com/openvie...9d1e5/1?pq-origsite=gscholar&cbl=18750&diss=y
Aura-biomes are present in the water layer above coral reef benthic macro-organisms
https://www.ncbi.nlm.nih.gov/pubmed/28828261
https://www.reef2reef.com/threads/e...ome-in-a-new-aquarium-using-live-rock.665936/
Elemental Analysis of Skimmate
https://reefs.com/magazine/elementa...-skimmer-actually-remove-from-aquarium-water/
Bacterial Counts in Reef Aquarium Water
https://reefs.com/magazine/bacteria...ing-and-granular-activated-carbon-filtration/
And here's some thought provoking papers:

Ammonium Uptake by Symbiotic and Aposymbiotic Reef Corals
http://www.ingentaconnect.com/content/umrsmas/bullmar/1979/00000029/00000004/art00011
Amino acids a source of nitrogen for corals
https://journals.biologists.com/jeb...2/Uptake-of-dissolved-free-amino-acids-by-the
Urea a source of nitrogen for corals
https://www.sciencedirect.com/science/article/abs/pii/S0022098105005538
Diazotrpophs a source of nitrogen for corals
https://pubmed.ncbi.nlm.nih.gov/27335448/
Context Dependant Effects of Nutrient Loading on the Coral-Algal Mutualism
https://www.researchgate.net/public...nutrient_loading_on_the_coral-algal_mutualism


https://www.cambridge.org/core/jour...reef-corals/AFB1CF4CB68823BD13AD254623FD3C7C#An Experimental Mesocosm for Longterm Studies of Reef Corals

Phosphate Deficiency:
Nutrient enrichment can increase the susceptibility of reef corals to bleaching:
https://www.nature.com/articles/nclimate1661
Ultrastructural Biomarkers in Symbiotic Algae Reflect the Availability of Dissolved Inorganic Nutrients and Particulate Food to the Reef Coral Holobiont:
https://www.frontiersin.org/articles/10.3389/fmars.2015.00103/full
Phosphate deficiency promotes coral bleaching and is reflected by the ultrastructure of symbiotic dinoflagellates
https://www.sciencedirect.com/science/article/pii/S0025326X17301601?via=ihub
Effects of phosphate on growth and skeletal density in the scleractinian coral Acropora muricata: A controlled experimental approach
https://www.sciencedirect.com/science/article/pii/S0022098111004588
High phosphate uptake requirements of the scleractinian coral Stylophora pistillata
http://jeb.biologists.org/content/214/16/2749.full
Phosphorus metabolism of reef organisms with algal symbionts
https://esajournals.onlinelibrary.w...98e60zfBEvx5IcIVGhmlpUYmzIJuqUNVm0sG8_0vth6lq
https://therichross.com/skeptical-reefkeeping-ix-test-kits-chasing-numbers-and-phosphate/

 

[Pankney72]

Google scholar has been very helpful for me and you'll see me posting refferneces alot. There are some good videos on youtube (and lots of not so good ones). Here's some links I have bookmakred if you're interested:


"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title (Paper back is ~$20, Kindle is ~$10), both deal with the conflicting roles of the different types of DOC in reef ecosystems. 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


Changing Seas - Mysterious Microbes


Nitrogen cycling in hte coral holobiont


BActeria and Sponges


Maintenance of Coral Reef Health (refferences at the end)


Optical Feedback Loop in Colorful Coral Bleaching


Richard Ross What's up with phosphate"


Indirect effects of algae on coral: algae‐mediated, microbe‐induced coral mortality
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2006.00937.x
Influence of coral and algal exudates on microbially mediated reef metabolism.
Coral DOC improves oxygen (autotrophy), algae DOC reduces oxygen (heterotrophy).
https://peerj.com/articles/108/?utm_source=TrendMD&utm_campaign=PeerJ_TrendMD_0&utm_medium=TrendMD
Role of elevated organic carbon levels and microbial activity in coral mortality
http://www.int-res.com/articles/meps2006/314/m314p119.pdf
Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity
Algae releases significantly more DOC into the water than coral.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027973
Pathologies and mortality rates caused by organic carbon and nutrient stressors in three Caribbean coral species.
Starch and sugars (doc) caused coral death but not high nitrates, phosphates or ammonium.
http://www.int-res.com/articles/meps2005/294/m294p173.pdf
Visualization of oxygen distribution patterns caused by coral and algae
https://peerj.com/articles/106/
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719127/
Microbial ecology: Algae feed a shift on coral reefs
https://www.nature.com/articles/nmicrobiol201661
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.
https://www.ncbi.nlm.nih.gov/pubmed/23303369
Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching
https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.13695
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)
https://www.sciencedirect.com/science/article/pii/S0166445X19307192
Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton
https://www.nature.com/articles/ismej2017142
Unseen players shape benthic competition on coral reefs.
https://www.ncbi.nlm.nih.gov/pubmed/22944243
Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.
https://www.ncbi.nlm.nih.gov/pubmed/27795310
Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.
https://www.ncbi.nlm.nih.gov/pubmed/22957055
Macroalgal extracts induce bacterial assemblage shifts and sublethal tissue stress in Caribbean corals.
https://www.ncbi.nlm.nih.gov/pubmed/23028648
Biophysical and physiological processes causing oxygen loss from coral reefs.
https://elifesciences.org/articles/49114.pdf
Global microbialization of coral reefs
DDAM Proven
https://www.nature.com/articles/nmicrobiol201642
Coral Reef Microorganisms in a Changing Climate, Fig 3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7096749/figure/fig3/
Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes
https://msystems.asm.org/content/msys/3/2/e00162-17.full.pdf

Because sponges are essential players in the carbon, nitrogen and phosphorus cycle(s) on reefs here's some links to research done with them.

Element cycling on tropical coral reefs.
This is Jasper de Geoij's ground breaking research on reef sponges. (The introduction is in Dutch but the content is in English.)
https://www.rug.nl/research/portal/files/14555035/13completethesis.pdf
Sponge symbionts and the marine P cycle
https://www.pnas.org/content/112/14/4191
Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges
https://www.pnas.org/content/112/14/4381
Differential recycling of coral and algal dissolved organic matter via the sponge loop.
Sponges treat DOC from algae differently than DOC from corals
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.12758
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.
https://www.researchgate.net/publication/279061640_2013_deGoeij_Science_Sponge_loop
Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934968/
The Role of Marine Sponges in Carbon and Nitrogen Cycles of COral Reefs and Nearshore Environments.
https://search.proquest.com/openvie...9d1e5/1?pq-origsite=gscholar&cbl=18750&diss=y
Aura-biomes are present in the water layer above coral reef benthic macro-organisms
https://www.ncbi.nlm.nih.gov/pubmed/28828261
https://www.reef2reef.com/threads/e...ome-in-a-new-aquarium-using-live-rock.665936/
Elemental Analysis of Skimmate
https://reefs.com/magazine/elementa...-skimmer-actually-remove-from-aquarium-water/
Bacterial Counts in Reef Aquarium Water
https://reefs.com/magazine/bacteria...ing-and-granular-activated-carbon-filtration/
And here's some thought provoking papers:

Ammonium Uptake by Symbiotic and Aposymbiotic Reef Corals
http://www.ingentaconnect.com/content/umrsmas/bullmar/1979/00000029/00000004/art00011
Amino acids a source of nitrogen for corals
https://journals.biologists.com/jeb...2/Uptake-of-dissolved-free-amino-acids-by-the
Urea a source of nitrogen for corals
https://www.sciencedirect.com/science/article/abs/pii/S0022098105005538
Diazotrpophs a source of nitrogen for corals
https://pubmed.ncbi.nlm.nih.gov/27335448/
Context Dependant Effects of Nutrient Loading on the Coral-Algal Mutualism
https://www.researchgate.net/public...nutrient_loading_on_the_coral-algal_mutualism


https://www.cambridge.org/core/jour...reef-corals/AFB1CF4CB68823BD13AD254623FD3C7C#An Experimental Mesocosm for Longterm Studies of Reef Corals

Phosphate Deficiency:
Nutrient enrichment can increase the susceptibility of reef corals to bleaching:
https://www.nature.com/articles/nclimate1661
Ultrastructural Biomarkers in Symbiotic Algae Reflect the Availability of Dissolved Inorganic Nutrients and Particulate Food to the Reef Coral Holobiont:
https://www.frontiersin.org/articles/10.3389/fmars.2015.00103/full
Phosphate deficiency promotes coral bleaching and is reflected by the ultrastructure of symbiotic dinoflagellates
https://www.sciencedirect.com/science/article/pii/S0025326X17301601?via=ihub
Effects of phosphate on growth and skeletal density in the scleractinian coral Acropora muricata: A controlled experimental approach
https://www.sciencedirect.com/science/article/pii/S0022098111004588
High phosphate uptake requirements of the scleractinian coral Stylophora pistillata
http://jeb.biologists.org/content/214/16/2749.full
Phosphorus metabolism of reef organisms with algal symbionts
https://esajournals.onlinelibrary.w...98e60zfBEvx5IcIVGhmlpUYmzIJuqUNVm0sG8_0vth6lq
https://therichross.com/skeptical-reefkeeping-ix-test-kits-chasing-numbers-and-phosphate/

Holy hell! You rock! This and the references in the stuff you posted will be plenty to keep me going! Wish I could like this twice.