. 2016 May 18;7:673. doi: 10.3389/fmicb.2016.00673

Table 1.

Common environmental processes catalyzed by microbial guilds.

Catalytic microbial guild	Catalyzed environmental process	Service/Application	Guild's model species	References
Aerobic heterotrophic bacteria	Organic carbon degradation (breakdown of suspended carbon to soluble carbon)	Organic matter removal from wastewater	Bacteroidetes α- and β- proteobacteria, Acidovorax spp., Fermicutes spp.	Wagner and Loy, 2002; Wagner et al., 2002; Das et al., 2011
	Organic carbon oxidation (soluble carbon to CO₂)	Organic matter removal from wastewater	Bacteroidetes α- and β- proteobacteria, Acidovorax spp., Fermicutes spp.	Wagner and Loy, 2002; Wagner et al., 2002; Das et al., 2011
	Proteolysis (organic nitrogen to NH $_{4}^{+}$ )	Global nitrogen cycle, organic matter removal from wastewater	Bacteroidetes α- and β- proteobacteria, Acidovorax spp., Fermicutes spp.	Wagner and Loy, 2002; Wagner et al., 2002; Das et al., 2011; Schreiber et al., 2012
Heterotrophic denitrifiers	Denitrification (NO $_{3}^{-}$ /NO $_{2}^{-}$ reduction to N₂)	Global nitrogen cycle, biological nitrogen removal from wastewater	Paracoccus denitrifican, Pseudomonas aeruginosa, Acidovorax spp., α-, and β- Proteobacteria	Ferguson, 1998; Brown, 2010; Kraft et al., 2011; Schreiber et al., 2012
Autotrophic nitrifiers, including both, ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)	Nitritation (NH $_{4}^{+}$ oxidation to NO $_{2}^{-}$ )	Global nitrogen cycle, nitrogen removal from wastewater	Nitrosomonas europaea, Nitrosomonas eutropha, Nitrosospira spp.	Hooper, 1991; Arp et al., 2002; Chain et al., 2003; Ferguson et al., 2007; Perez-Garcia et al., 2014b
	Nitratation (NO $_{2}^{-}$ oxidation to NO $_{3}^{-}$ )	Global nitrogen cycle, nitrogen removal from wastewater	Nitrospira defluvii, Nitrobacter spp.	Freitag and Bock, 1990; Ferguson et al., 2007; Lücker et al., 2010; Schreiber et al., 2012
	Nitrifier denitrification and hydroxylamine incomplete oxidation (production of NO and N₂O)	Production and emission green house and ozone depleting gases	Nitrosomonas europaea, Nitrosomonas eutropha	Shaw et al., 2006; Yu et al., 2010; Chandran et al., 2011; Schreiber et al., 2012
Anaerobic ammonium oxidizers (ANAMMOX)	Ammonium oxidation to di-nitrogen gas (NH $_{4}^{+}$ oxidation to N₂)	Global nitrogen cycle, nitrogen removal from wastewater	Kuenenia stuttgartiensis, Candidatus Jettenia asiatica, Brocardia anammoxidans	Kuypers et al., 2003; Kuenen, 2008; Hu et al., 2012
Glycogen accumulating organisms (GAOs)	Anaerobic glycogen formation (carbon uptake and storage compound formation without phosphorus release)	Phosphorus removal from wastewater	Micropruina glycogenica, Tetrasphaera spp., Amaricoccus spp.	Seviour et al., 2003; de-Bashan and Bashan, 2004; Martín et al., 2006; Wilmes et al., 2008
Phosphate accumulating organisms (PAOs)	Anaerobic phosphorus release (hydrolysis of intracellular polyphosphates for carbon uptake and storage compound formation)	Phosphorus removal from wastewater	Acinetobacter spp., Microlunatus phosphovorus, Clostridium spp., Candidatus Accumulibacter phosphatis	Seviour et al., 2003; de-Bashan and Bashan, 2004; Martín et al., 2006; Wilmes et al., 2008
	Aerobic phosphorus uptake (storage compound degradation accompanied by soluble phosphorus uptake)	Phosphorus removal from wastewater	Acinetobacter spp., Microlunatus phosphovorus, Candidatus Accumulibacter phosphatis	Seviour et al., 2003; de-Bashan and Bashan, 2004; Martín et al., 2006; Wilmes et al., 2008
Polyhydroxyalkanoates (PHA) accumulating bacteria	Anaerobic formation of carbon storage compounds in form of polymers of the PHA family	Polyhydroxybutyrate (PHB) base bioplastic production	Pseudomonas oleovorans, Alcaligenes eutrophus, Azotobacter vinelandii, Alcaligenes latus	Batstone et al., 2003; Patnaik, 2005; Dias et al., 2008
Hydrogen producing acetogenic bacteria/archea	Fermentation of higher organic acids to produce acetate, H_2, and CO₂	Hydrogen and methane production	Clostridium spp., Syntrophomonadaceae spp., Bacteriodetes	Hatamoto et al., 2007; Rittmann et al., 2008; Khanal, 2009a,b
Autotrophic homoacetogenic bacteria	Syngas fermentation (use of hydrogen carbon monoxide and dioxide as carbon and energy source)	Ethanol, butanol, methane and small chain fatty acid production	Clostridium ljungdahlii	Khanal, 2009b; Abubackar et al., 2011
Heterotrophic homoacetogenic bacteria	Fermentation of higher organic acids and alcohols to produce acetate and CO₂	Methane production	Streptococcaceae and Enterobacteriaceae families, Clostridium aceticum, Acetobacterium woodii, and Bacteroidetes spp., Clostridium spp., Lactobacillus spp.	Hatamoto et al., 2007; Rittmann et al., 2008; Khanal, 2009a,b
Anaerobic methanogenic archea	Acetotrophic conversion of acetate to methane	Methane production	Methanosarcina spp. and Methanosaeta spp.	(Hatamoto et al., 2007; Rittmann et al., 2008; Khanal, 2009a,b)
	Hydrogenotrophic conversion of carbon dioxide to methane	Methane production	Methanosarcina spp	Hatamoto et al., 2007; Rittmann et al., 2008; Khanal, 2009a,b
Photo-autotrophs (Microalgae/Cyanobacteria)	Nutrient assimilation (soluble N & P assimilation to organic molecules)	Eutrophication of water bodies, nutrient removal from wastewater	Clamydomonas reinhardtii, Chlorella vulgaris, Spirulina platensi, Microcystis aeruginosa, Anabaena spp., Oscilatoria spp., Nostoc spp.	de-Bashan and Bashan, 2004, 2010; Perez-Garcia et al., 2010
	Autotrophic CO₂ fixation (CO₂ fixation to biomass)	Global carbon cycle, biomass formation, CO₂ sequestration	Clamydomonas reinhardtii, Chlorella spp., Spirulina platensi, Microcystis aeruginosa, Scenedesmus obliquus, Nanochloropsis spp.	Das et al., 2011; Cheirsilp and Torpee, 2012; Girard et al., 2014; Wu et al., 2015
	Autotrophic and heterotrophic lipid, starch and pigments production	Biofuels and valuable chemical production	Chlorella vulgaris, Chlorella prototecoides	de-Bashan et al., 2002; Perez-Garcia et al., 2011; Choix et al., 2012a,b; Perez-Garcia and Bashan, 2015
	Production of nitrous and nitrous oxides	Production and emission green house and ozone depleting gases	Chlorella vulgaris	Guieysse et al., 2013; Alcántara et al., 2015
	Synthesis of exo-polymers	Bio-absorption of organic compounds and pollutants	Clamydomonas reinhardtii, Chlorella vulgaris, Spirulina platensis.	Markou and Georgakakis, 2011; Subashchandrabose et al., 2013
Cyanobacteria	Production and realize of secondary metabolites and toxic organic compounds (microcystin, nodularin, cylindrospermopsin, among others)	Self-population an grazer organism control	Microcystis aeruginosa, Anabaena spp., Oscilatoria spp., Nostoc spp.	Welker and Von Döhren, 2006; Yadav et al., 2009; Kaplan et al., 2012; Dittmann et al., 2013; Neilan et al., 2013
Dissimilatory metal-reducing bacteria.	Anaerobic Fe³⁺ reduction to Fe²⁺ (reduction of insoluble iron to soluble form)	Global iron cycle, bioremediation of metallic pollutants in soil and groundwater	Geobacter metallireducens, Geobacter sulfurreducens, Albidoferax ferrireducens, Shewanella putrefaciens	Lovley and Coates, 1997; Malik, 2004; Gadd, 2010; Melton et al., 2014
	Anaerobic Mn⁴⁺ reduction to Mn²⁺ (reduction of insoluble iron to soluble form)	Global iron cycle, bioremediation of metallic pollutants in soil and groundwater	Geobacter metallireducens, Geobacter sulfurreducens, Albidoferax ferrireducens, Shewanella putrefaciens	Lovley and Coates, 1997; Malik, 2004; Gadd, 2010; Melton et al., 2014
	Anaerobic As⁵⁺ reduction to As³⁺ (reduction of insoluble arsenic to soluble)	Bioremediation of metallic pollutants in soil	Geospirillum arsenophilus, Geospirillum barnseii, Chrysiogenes arsenatis, Sulfurospirillum strain NP4	Lovley and Coates, 1997; Malik, 2004; Lear et al., 2007; Gadd, 2010
	Aerobic Hg²⁺ reduction to Hg⁰ (reduction of soluble mercury to volatile form)	Bioremediation of metallic pollutants in soil and water	Pseudomonas spp.	Lovley and Coates, 1997
	Anaerobic U⁶⁺ reduction to U⁴⁺ (reduction of soluble uranium to insoluble form)	Soil bioremediation of radioactive pollutants	Thiobacillus thiooxidan, Rhodoferax ferrireducens, Geobacter sulfurreducens, Shewanella putrefaciens, Desulfotomaculum reducens	Lovley and Coates, 1997; Malik, 2004; Gadd, 2010
	Anaerobic Tc⁴⁺ reduction to Tc⁷⁺ (reduction of soluble technecium to poorly soluble form)	Soil bioremediation of radioactive pollutants	Geobacter spp.	Lear et al., 2010
	Anaerobic and aerobic Cr⁶⁺ reduction to Cr³⁺ (reduction of soluble chromium to insoluble form)	Bioremediation of metallic pollutants in soil and water	Pseudomonas spp., Achromobacter Eurydice, Desulfovibrio vulgaris, Bacillus spp., Desulfotomaculum reducens	Wang and Shen, 1995; Lovley and Coates, 1997; Malik, 2004; Gadd, 2010
Heavy metal resistant microbes	Heavy metal (Cu, Zn, Ni, Cd, Pb, Hg) immobilization by biosorption, bioaccumulation, biochelation	Bioremediation of metallic pollutants in soil and water	Alcaligenes eutrophus, Alcaligenes xylosoxidans, Stenotrophomonas sp., Ralstonia eutropha, Staphylococcus sp., Pseudomonas syringae	Lovley and Coates, 1997; Diels et al., 1999; Malik, 2004; Gadd, 2010; Edwards and Kjellerup, 2013
Dissimilatory sulfate reducing bacteria	Anaerobic SO $_{4}^{2 -}$ reduction to H₂S (reduction of soluble and insoluble sulfur to volatile form)	Global sulfur cycle, treatment of sulfur and sulfate contaminated groundwater and industrial wastewater	Desulfovibrio spp., Thermodesulfovibrio yellowstonii, Archaeoglobus spp., Desulfatibacillum spp. Desulfothermus spp., Desulfotomaculum reducens	Lovley and Coates, 1997; Malik, 2004; Gadd, 2010; Pereira et al., 2011; Hao et al., 2014
Sulfur oxidizing bacteria	Chemiolitotrophic H₂S, S⁰ oxidation to SO $_{4}^{2 -}$ (reduction of soluble and insoluble sulfur to volatile form)	Global sulfur cycle, bioremediation of sulfur pollutants in water	Beggiatoa spp., Thiobacillus novellus, Sulfolobus spp., Purple and green sulfur-oxidizing bacteria	Lovley and Coates, 1997; Kappler et al., 2000; Malik, 2004; Gadd, 2010; Pokorna and Zabranska, 2015
Iron oxidizing bacteria	Chemiolitotrophic Fe²⁺ oxidation to Fe³⁺ (oxidation of soluble iron to insoluble form)	Global iron cycle, bioremediation of metallic pollutants in water	Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, Sulfobacillus thermosulfidooxidans	Lovley and Coates, 1997; Malik, 2004; Gadd, 2010
Ectomycorrhizal fungi	Filamentous (hyphae) extension of plant root systems (do not penetrate plant root cells)	Enhance plant acquisition of nitrogen, minerals and water	Russula xerampelina, Amanita francheti, Suillus bovinus	Gardes and Bruns, 1996; Chalot and Brun, 1998; Reid and Greene, 2012
Arbuscular mycorrhizae fungi	Filamentous (hyphae) extension of plant root systems (penetrate plant root cells)	Enhance plant acquisition of nutrients, minerals and water	Rhizophagus Irregularis, Piriformospora indica	Reid and Greene, 2012
Endophytic fungi	Fungi-plant symbiotic production of bioactive compounds	Pathogen and predator resistance	Clavicipitaceae family	Reid and Greene, 2012
Lignocellulosic fungi	Lignin degradation to soluble carbohydrates mediated by peroxidases and laccase	Global carbon cycle, lignocellulosic biomass degradation, biofuel production, bio-refining of valuable chemicals	Phanerochaete chrysosporium, Pleurotus spp., Trametes versicolor, Phanerochaete chrysosporium	Bugg et al., 2011; Harms et al., 2011
	Organic pollutant degradation to harmless compounds mediated by peroxidase, laccase and cytochromes	Organic pollutant degradation, bioremediation	Gloeophyllum spp., Trabeum spp., Gliocladium virens, Trametes versicolor, Phanerochaete chrysosporium, Candida spp.	Keller et al., 2005; Bugg et al., 2011; Harms et al., 2011; Lah et al., 2011; Margot et al., 2013
Recalcitrant pollutant degrading bacteria	Organic pollutant degradation to harmless compounds mediated by peroxidase, laccase, and cytochromes	Organic pollutant degradation (pesticides, pharmaceuticals, agrochemicals, industrial waste chemicals, oil, and petrochemicals)	Pseudomonas spp., Streptomyces spp., Desulfovibrio spp., Brevundimonas diminuta,	Díaz, 2004; Head et al., 2006; Singh, 2009; Guazzaroni and Ferrer, 2011; Nikel et al., 2014
Plant growth promoting bacteria (PGPB)	Diazotrophic nitrogen fixation (di-nitrogen gas conversion to ammonia, which is available for plant assimilation)	Global nitrogen cycle, increase biomass production yields of plants or microalgae	Azospirillum brasilense, Azospirillum lipoferum, Bacillus pumilus, Azoarcus sp., Rhizobium leguminosarum	Hartmann and Bashan, 2009; Hernandez et al., 2009; Reid and Greene, 2012
Plant and microalgae promoting bacteria	Phytohormone production (indole-3-acetic acid and gibberellin production)	Increase of starch formation, and ammonium and phosphate uptake by microalgae	Azospirillum brasilense, Bacillus pumilus	de-Bashan et al., 2002, 2005, 2011; Choix et al., 2012a, 2014; Meza et al., 2015a,b

Communities' microbial guilds can be modeled using metabolic networks by rendering genomic data of model species enlisted in the fourth column.