Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling

Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity

Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.

Development of Nitrogen Recycling Strategies for Bioregenerative Life Support Systems in Space

To enable long-distance space travel, the development of a highly efficient and robust system to recover nutrients from waste streams is imperative. The inability of the current physicochemical-based environmental control and life support system (ECLSS) on the ISS to produce food in situ and to recover water and oxygen at high enough efficiencies results in the need for frequent resupply missions from Earth. Therefore, alternative strategies like biologically-based technologies called bioregenerative life support systems (BLSSs) are in development. These systems aim to combine biological and physicochemical processes, which enable in situ water, oxygen, and food production (through the highly efficient recovery of minerals from waste streams). Hence, minimalizing the need for external consumables. One of the BLSS initiatives is the European Space Agency's (ESA) Micro-Ecological Life Support System Alternative (MELiSSA). It has been designed as a five-compartment bioengineered system able to produce fresh food and oxygen and to recycle water. As such, it could sustain the needs of a human crew for long-term space exploration missions. A prerequisite for the self-sufficient nature of MELiSSA is the highly efficient recovery of valuable minerals from waste streams. The produced nutrients can be used as a fertilizer for food production. In this review, we discuss the need to shift from the ECLSS to a BLSS, provide a summary of past and current BLSS programs and their unique approaches to nitrogen recovery and processing of urine waste streams. In addition, compartment III of the MELiSSA loop, which is responsible for nitrogen recovery, is reviewed in-depth. Finally, past, current, and future related ground and space demonstration and the space-related challenges for this technology are considered.

Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems

Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application. To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs (Acidovorax delafieldii, Comamonas testosteroni, Cupriavidus necator, Delftia acidovorans, Pseudomonas fluorescens, and Vibrio campbellii) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium (Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm^-1, while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with C. necator and V. campbellii resulted in a complete halt of the urea hydrolysis process, while in the case of A. delafieldii incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.

Effect of alkalinity on bio-zeolite regeneration in treating cold low-strength ammonium wastewater via adsorption and enhanced regeneration

Low temperature severely inhibits microbial activity, making biological method inefficient for ammonium removal from wastewater. A zeolite biological fixed-bed (ZBFB) was successfully established for 6.0-8.0 °C low-strength ammonium wastewater treatment via adsorption-regeneration. Ion exchange was a remarkable alternative and zeolite was mostly applied. Nevertheless, insufficient zeolite bio-regeneration rate was the key obstacle for economically sustainable utilization. By adsorption, effluent NH₄⁺-N was around 1.5-2.5 mg/L. About 26% regeneration rate was obtained. With a ceramsite biological aerobic filter (CBAF) operated with ZBFB in series at the regeneration stage, the regeneration rate reached 95%, 3.5 times higher. Studies of alkalinity effects on bio-zeolite regeneration process indicated that Na₂CO₃ worked better than NaHCO₃. Greater amount and one dose mode of alkalinity addition, higher regeneration rate could be obtained. The bio-zeolite regeneration process followed pseudo first-order kinetics with K = 0.0629 h^-1. High-throughput sequencing analysis indicated the enriched nitrifying microorganisms in CBAF fully oxidized NH₄⁺-N in regeneration solution, which accelerated desorption and conversion of NH₄⁺-N by the circulation of regeneration solution between ZBFB and CBAF. The dynamic adsorption experiment proved that ZBFB-CBAF was feasible for cold low-strength ammonium wastewater treatment.

A novel process of the isolation of nitrifying bacteria and their development in two different natural lab-scale packed-bed bioreactors for trichloroethylene bioremediation

Trichloroethylene (TCE) is a carcinogenic compound that is commonly present in groundwater and has been detected in drinking water sources for Mexican towns in the Mexico-US border area. Nitrifying bacteria, such as Nitrosomonas europaea, have been shown to be capable of degrading halogenated compounds, including TCE, but it is difficult to obtain high cell concentrations of these bacteria. The aim of the present study was to generate biomass of a nitrifying bacterial consortium from the sludge of an urban wastewater treatment plant (WWTP) and evaluate its capacity to biodegrade TCE in two different natural lab-scaled packed bed bioreactors. The consortium was isolated by a novel method using a continuous stirred-tank bioreactor inoculated with activated sludge from the Domos WWTP located in Cd. Obregón, Sonora, Mexico. The bioreactor was fed with specific media to cultivate ammonia-oxidizing bacteria at a dilution rate near the maximum specific growth rate reported for Nitrosomonas europaea. Optical density and suspended solids measurements were performed to determine the culture biomass production, and the presence of inorganic nitrogen species was determined by spectrophotometry. The presence of nitrifying ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was confirmed by PCR amplification, and biofilm formation was observed by scanning electron microscopy. Batch-scale experiments confirmed the biodegradative activity of the isolated consortium, which was subsequently fixed in an inorganic carrier as zeolite and a synthetic carrier such as polyurethane to both be used as lab-scale packed-bed bioreactors, with up to 58.63% and 62.7% of TCE biodegradation achieved, respectively, demonstrating a possible alternative for TCE bioremediation in environmental and engineering systems.

Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp

Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm^-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi’s nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm^-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm^-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm^-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.

Evaluating the feasibility of ratio control strategy for achieving partial nitritation in a continuous floccular sludge reactor: Experimental demonstration

To investigate the applicability of ratio control strategy to other systems, a continuous floccular sludge reactor was used in this study. It was found that nitrite accumulation was barely detected throughout 70days' investigation, being the average concentration in the effluent of 0.7±0.4mg/L. Batch experiments indicated that low dissolved oxygen (DO<0.3mg·L^-1) greatly repressed the ammonium oxidizing bacteria (AOB) but only slightly inhibited the nitrite oxidizing bacteria (NOB). However, high-throughput sequencing revealed that the ratio of abundance between Nitrospira and Nitrosomonas, being the dominant NOB and AOB respectively, was considerably low (1.2%/18.7%). The weak oxygen gradients in floccular sludge and the selectively enriched K-strategist NOB Nitrospira under oxygen-limited conditions were both contributed to the failure of achieving partial nitritation; therefore, the rapid start-up of partial nitritation process based on proposed ratio control strategy is not feasible for continuous floccular sludge systems treating low-strength wastewater.

Growth modelling of Nitrosomonas europaea ATCC® 19718 and Nitrobacter winogradskyi ATCC® 25391: A new online indicator of the partial nitrification

The aim of the present work was to study the growth of two nitrifying bacteria. For modelling the nitrifying subsystem of the MELiSSA loop, Nitrosomonas europaea ATCC® 19718 and Nitrobacter winogradskyi ATCC® 25931 were grown separately and in cocultures. The kinetic parameters of a stoichiometric mass balanced Pirt model were identified: μmax=0.054h(-1), decay rate b=0.003h(-1) and maintenance rate m=0.135gN-NH4(+)·gX(-1)·h(-1) for Nitrosomonas europaea; μmax=0.024h(-1), b=0.001h(-1) and m=0.467gN-NO2(-)·gX(-1)·h(-1) for Nitrobacter winogradskyi. A predictive structured model of nitrification in co-culture was developed. The online evolution of the addition of KOH is correlated to the nitritation; the dissolved oxygen concentration is correlated to both nitritation and nitratation. The model suitably represents these two variables so that transient partial nitrification is assessed. This is a clue for avoiding partial nitrification by predictive functional control.

Understanding, Monitoring, and Controlling Biofilm Growth in Drinking Water Distribution Systems

In drinking water distribution systems (DWDS), biofilms are the predominant mode of microbial growth, with the presence of extracellular polymeric substance (EPS) protecting the biomass from environmental and shear stresses. Biofilm formation poses a significant problem to the drinking water industry as a potential source of bacterial contamination, including pathogens, and, in many cases, also affecting the taste and odor of drinking water and promoting the corrosion of pipes. This article critically reviews important research findings on biofilm growth in DWDS, examining the factors affecting their formation and characteristics as well as the various technologies to characterize and monitor and, ultimately, to control their growth. Research indicates that temperature fluctuations potentially affect not only the initial bacteria-to-surface attachment but also the growth rates of biofilms. For the latter, the effect is unique for each type of biofilm-forming bacteria; ammonia-oxidizing bacteria, for example, grow more-developed biofilms at a typical summer temperature of 22 °C compared to 12 °C in fall, and the opposite occurs for the pathogenic Vibrio cholerae. Recent investigations have found the formation of thinner yet denser biofilms under high and turbulent flow regimes of drinking water, in comparison to the more porous and loosely attached biofilms at low flow rates. Furthermore, in addition to the rather well-known tendency of significant biofilm growth on corrosion-prone metal pipes, research efforts also found leaching of growth-promoting organic compounds from the increasingly popular use of polymer-based pipes. Knowledge of the unique microbial members of drinking water biofilms and, importantly, the influence of water characteristics and operational conditions on their growth can be applied to optimize various operational parameters to minimize biofilm accumulation. More-detailed characterizations of the biofilm population size and structure are now feasible with fluorescence microscopy (epifluorescence and CLSM imaging with DNA, RNA, EPS, and protein and lipid stains) and electron microscopy imaging (ESEM). Importantly, thorough identification of microbial fingerprints in drinking water biofilms is achievable with DNA sequencing techniques (the 16S rRNA gene-based identification), which have revealed a prevalence of previously undetected bacterial members. Technologies are now moving toward in situ monitoring of biomass growth in distribution networks, including the development of optical fibers capable of differentiating biomass from chemical deposits. Taken together, management of biofilm growth in water distribution systems requires an integrated approach, starting from the treatment of water prior to entering the networks to the potential implementation of "biofilm-limiting" operational conditions and, finally, ending with the careful selection of available technologies for biofilm monitoring and control. For the latter, conventional practices, including chlorine-chloramine disinfection, flushing of DWDS, nutrient removal, and emerging technologies are discussed with their associated challenges.

Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions

In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4(+)-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

Conditions for partial nitrification in biofilm reactors and a kinetic explanation

Nitrification is a two-step process in which ammonia is incompletely oxidized by ammonia-oxidizing bacteria or archaea (AOB) to nitrite, which is then further oxidized to nitrate by nitrite-oxidizing bacteria (NOB). Literature reports show that segregation of initially coexisting ammonia and nitrite oxidizing populations co-immobilized in gel cubes and cultured in a set-up with three reactors in series (without recirculation) is attained. In those studies NOB were present and nitrite was oxidized mainly in the last reactor. We developed a mathematical model for immobilized biomass that allows for one-dimensional gradients of metabolites and changes of porosity within the gel due to growth. The model reproduced the experimentally observed compartmentalization under the conditions used by Noto et al. (Noto et al., 1998. Water Res 32(3): 769- 773), using standard kinetic parameters of nitrifying bacteria including free ammonia inhibition of AOB and NOB. The model predicted compartmentalization when the ammonium load was sufficiently high and liquid phase mixing sufficiently limited (close to plug-flow). Modeling results demonstrated that inhibition of NOB by free ammonia did not substantially contribute to the compartmentalization in biofilm reactors. Additional simulations identified the higher oxygen affinity of AOB as the key parameter leading to compartmentalization (i.e., partial nitrification) in artificial and natural biofilms since they enable the formation of oxygen gradients. As a result, a tendency for compartmentalization was found even at equal competitiveness.