Nitrosomonas species also known as Ammonia Oxidizing Bacteria (AOB) have always been discussed as obligate aerobic chemoautotrophs. Under aerobic conditions, the Nitrosomonas convert ammonia  to nitrite while using carbon dioxide  and carbonate as a carbon source. 

I have recently read multiple peer reviewed papers that document the ability of Nitrosomonas to utilize various organic compounds as an energy source with nitrite as an alternative electron acceptor - producing N2 gas as a final product. This ability to use their waste product from aerobic reactions as an electron acceptor reveals how Nitrosomonas can survive in systems with substantial anoxic periods.

Here is a link to a 2009 paper with more details:
 https://www.ncbi.nlm.nih.gov/pubmed/19452213

Easily seen using a phase contrast microscope, filamentous bacteria provide the structural support on which floc forming organisms grow.  Without filaments, floc tends to shrink in size and be more susceptible to sheer.   Problems arise when filaments become overabundant and extend from the floc.  Once extended from floc and reducing floc density, filaments begin inhibiting settling rates.  So like many things, filaments are good in moderation but bad when overabundant.  What conditions promote filamentous growth?

• Low Dissolved Oxygen (D.O.)
• High influent soluble BOD & organic acids (causing a zone of highly depressed DO near the influent)
• Sulfides - several filamentous forms can also obtain energy from sulfide oxidation
• Low nitrogen or phosphorus - unbalanced C:N:P ratio
• Grease & Long chain fatty acids - this encourages Nocardia type foaming 

Some of the above problems can be fixed which reduces growth conditions favorable for filaments.  Consider corrective measures such as:

• Moving more aeration to the inlet area to avoid the DO depression often seen near the influent
• A long term solution is to step-feed influent which prevents DO drop and high concentrations of organic acids (also known as septicity in influent)
• Add nutrients if C:N:P ratio is triggering filaments (they have more surface area to uptake scarce nutrients)
• Adjust F/M or MCRT 
• Using hypochlorite, peroxide, or other oxidant to disrupt the filaments.  This is only for severe problems.  With more surface area, filaments are more susceptible to disinfection than floc forming bacteria.  Dosing can be determined by jar testing and looking for filament disruption prior to disinfection of the main system.

We sure love to use acronyms in environmental science and wastewater treatment. I have had full discussions with people mistaking "the nitrifiers" for "denitrifiers" when speaking - think about how close the words sound in normal speech. So, I thought a list of terms would help get everyone on the same page.

• Ammonia Oxidizing Bacteria (AOB) - these organisms convert ammonia (NH3) into nitrite (NO2)
• Nitrite Oxidizing Bacteria (NOB) - organisms converting nitrite (NO2) into nitrate (NO3)
  
• Denitrifying Organisms - many species can use nitrate (fewer nitrite) under anoxic conditions
  
• Anammox - or Anaerobic Ammonia Oxidation is biochemical pathway that has NO2 + NH4 --> N2 (gas) + H2O. This is an anaerobic process that requires a long MCRT & low F/M conditions. Often a fixed film with anammox cultures is required for significant development.
  
• Comammox - abbreviation for Complete Ammonia Oxidation - some organisms such as Nitrospira have the ability to completely convert ammonia into nitrate. Instead of two distinct microbial populations, Comammox have a single population completely removing problem nitrogen forms.
  
• Feammox - (the latest identified reactions) - iron reducing organisms work at lower pH without oxygen. Ammonia oxidation with concurrent Iron III reduction produces energy for this class of organisms. Research is still in the early phase regarding these organisms and their potential in waste treatment.
  

MBR systems use membrane separation instead of a DAF or clarifier to remove biological solids from effluent wastewater. MBR systems are becoming more common as membrane technology has improved and overall costs are lower when compared with larger foot print activated sludge systems. When compared with extended aeration activated sludge units, MBR systems typically have the following differences:

• Higher MLSS/MLVSS 
• Smaller aeration basin & overall foot print
• Better control of F/M & MCRT
• Fewer problems with solids in effluent

The MBR is technologically superior to older clarifier systems, but they still have issues that require operator attention. First since a membrane separates solids from discharged water, settling rates and floc formation would not seem as critical - however biological polymers are just as important for good MBR function as they are in systems with conventional clarification. Why do I say that floc formation is just as important in an MBR with advanced membrane technology?

Pores in the membrane allow for water to pass with solids being retained. As pores become clogged with solids - both biological & particulate - the system goes into a backwash cycle to clear the pores and restore membrane function. The problem is that backwashing is not perfect, overtime pores deteriorate with accumulated solids. Even with cleaning technologies that include oxidants, acids, or enzymes - the pores will eventually become plugged. 

A leading cause of plugged pores in biological waste treatment units is the accumulation of high molecular weight and "sticky" biological polymers. Organisms that thrive in the low F/M conditions found in MBR systems also tend to excrete copious amounts of extracellular polymeric substances (EPS). While some EPS is good and improves separation potential, the wrong EPS and overabundance of EPS can both create blinding conditions in membrane pores. 

The easiest ways to monitor EPS in a biological treatment unit is to run SV30, SVI, and microscopic exam on at least a daily basis. Additional monitoring with molecular testing is equally important - including both Microbial Community Analysis (MCA) and qPCR for specific problem or good organisms which gives earlier warnings for EPS blinding potential. When you have a buildup of problematic EPS, do not just assume that it cannot be corrected. Multiple control methods exist, it is just best to address the EPS problem before membrane issues start to compromise unit performance.