Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

Table 1

Microorganisms identified in RAS biofilter component related with freshwater.

Group	Microorganism	Process	References
Actinobacteria	Microbacterium imperiale		[30]
	Mycobacterium chitae		[30]
	Corynebacterium tuberculostearicum	Pathogen in humans	[39]
	Propionibacterium acnes		[39]
Acidobacteria	Acidobacteria bacterium		[39]
Bacteroidetes	Chryseobacterium  sp.	Some strains pathogen in humans	[37]
	Flavobacteriales bacterium	Sulfate reduction	[37]
	Flavobacterium columnare	Pathogen in fish	[39]
	Flavobacterium  sp.	Heterotrophic denitrification	[38, 39]
	Bacteroides plebeius	Sulfate reduction	[39]
	Myroides  sp.	Pathogen in humans	[37]
	Sphingobacterium  sp.	Pathogen in fish	[30, 37, 39]
	Flectobacillus	Heterotrophic bacteria	[39]
-Proteobacteria	Agrobacterium tumefaciens	Pathogen in superior plants/nitrogen fixation	[30]
	Filomicrobium fusiforme		[30]
	Hyphomicrobium facilis		[30, 39]
	Hyphomicrobium denitrificans  sp.	Heterotrophic denitrification	[30]
	Nitrobacter winogradskyi	Nitrite oxidation	[30, 40]
	Nordella oligomobilis		[30]
	Ochrobactrum anthropi		[30]
	Rhizobium  sp.	Nitrogen fixation	[30, 37, 39]
	Rhodopseudomonas acidophila		[30]
	Rhodovulum euryhalinum	Denitrification	[30]
	Bradyrhizobium japonicum		[39]
	Woodsholea maritima		[39]
	Rhodobacter  sp.	Autotrophic denitrification/nitrogen fixation	[22, 30]
-Proteobacteria	Aquaspirillum  sp.	Pathogen in fish	[37]
	Comamonas	Heterotrophic denitrification/pathogen in fish	[22, 37, 39]
	Azovibrio restrictus		[30]
	Thiobacillus thioparus	Ammonia oxidation	[30]
	Herbaspirillum  sp.		[39]
	Ideonella dechloratans	Heterotrophic bacteria	[39]
	Rhodoferax fermentans	Autotrophic denitrification	[30]
	Nitrosomonas aestuarii	Anammox	[38]
	Nitrosomonas marina	Anammox	[16]
	Nitrosomonas oligotropha	Anammox	[38]
-Proteobacteria	Gemmatimonas aurantiaca		[39]
	Acinetobacter  sp.	Heterotrophic bacteria	[37, 39]
	Aeromonas  sp.	Heterotrophic denitrification/pathogen in fish and humans	[37, 39]
	Pseudomonas  sp.	Heterotrophic denitrification/pathogen in fish and humans	[16, 22, 37, 39]
	Marinobacter  sp.		[39]
	Vibrio  sp.		[39]
	Edwardsiella  sp.	Pathogen in fish	[37]
-Proteobacteria	Arcobacter nitrofigilis	Nitrogen fixation	[39]
Firmicutes	Bacillus  sp.	Pathogen in fish	[37]
	Lactobacillus paraplantarum		[30]
	Lactococcus lactis		[39]
	Macrococcus brunensis		[30]
	Macrococcus lamae		[30]
	Sarcina  sp.	Dissimilatory nitrate reduction to ammonium (DNRA)	[37]
Sphingobacteria	Flexibacter  sp.		[30, 39]
	Runella slithyformis		[39]
Verrucomicrobia	Verrucomicrobia spinosum		[39]
Planctomycetes	Pirellula staleyi	Anammox	[30, 41]
	Planctomycetales  sp.	Anammox	[38]
	Planctomyces maris	Anammox	[38]
	Planctomicetes  sp.	Nitrite oxidation	[38]
Nitrospirae	Nitrospira moscoviensis	Nitrite oxidation	[30, 38, 39]

All microorganisms of this table were analysed with 16S rRNA clone library method, denaturing gradient gel electrophoresis (DGGE), and few cases with biochemical procedures.