The cryptic sponges in your system will process the labile DOC excreted by corals and algae1000X faster than the bacterioplankton removed by skimmers. Cryptic sponges also process the hydrophilic stuff skimmers don't address. Additionally, it doesn't matter where you look, sustanable farming or our owm physical and mental health, healthy microbiomes are essential. Feldman, et al, showed skimmers radically alter the microbiomes in reef aquariums so I don't see how skimmers can help keep most corals and reef aquariums for their normal life expectancies.
Here's some of my skimmerless ssytems:
https://youtu.be/4t8IjelZwUk
https://youtu.be/_Uf5IyXvajg
https://youtu.be/dh_nLhj1QXc
https://youtu.be/aCRYfIZs8N8
Dissolved Organic Carbon (DOC, aka carbon dosing) is a very complex subject in reef systems. Here's more inmformation 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
https://www.youtube.com/watch?v=-R2BMEfQGjU
Changing Seas - Mysterious Microbes
https://www.youtube.com/watch?v=c7hsp0dENEA
Nitrogen cycling in hte coral holobiont
https://youtu.be/DWItFGRQJL4
BActeria and Sponges
https://www.youtube.com/watch?v=-oLDclO7UcM
Maintenance of Coral Reef Health (refferences at the end)
https://youtu.be/dGIPveFJ_0Q
Optical Feedback Loop in Colorful Coral Bleaching
https://youtu.be/oadKezUYkJE
Richard Ross What's up with phosphate"
https://youtu.be/ZRIKW-9d2xI
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
And since we're discussing favorable and not so favorable bacteria here's a paper looking at how different corals and polyps are influencing the bacteria in the water column.
Aura-biomes are present in the water layer above coral reef benthic macro-organisms
https://www.ncbi.nlm.nih.gov/pubmed/28828261