Analysis of size distribution and areal cell density of ammonia-oxidizing bacterial microcolonies in relation to substrate microprofiles in biofilms

Influence of ammonia nitrogen management strategies on microbial communities in biofloc-based aquaculture systems

Controlling ammonia nitrogen is very important in intensive aquaculture. This study evaluated how different management strategies, i.e., chemoautotrophic (control), heterotrophic bacterial enhancement using carbon in glucose or polyhydroxy butyrate-hydroxy valerate (PHBV), and mature biofloc application, affect water quality and microbial community structure and composition. The management strategies were examined during the domestication and fish culture stages. In the domestication stage, the average NO2--N concentration, pH, and DO in the glucose-added groups were significantly lower than those in the control and PHBV groups. All water quality parameters differed significantly among treatment groups in the culture stage. Carbon additions decreased both bacterial richness and diversity in the fish culture stage. Both principal coordinate analysis and hierarchical cluster analysis grouped the 33 bacteria community samples from the two stages into four clusters, which were closely related to management strategy. The dominant taxa of the clusters were identified using linear discriminant analysis effect size (LEfSe). The biomarkers of Cluster I included Marinomonas, Photobacterium, and Vibrio. Porticoccus and Clade-1a were identified as the biomarkers of Cluster II. Marivia, Leucothrix, and Phaeodactylibacter were identified as the biomarkers of Cluster IV. The Cluster I biomarkers were positively correlated with NO2--N, while those of Cluster IV were positively correlated with NO3--N. The redundancy analysis showed that the bacterial communities and biomarkers were influenced by water quality parameters. Quantitative real-time PCR analysis revealed significant differences in the abundances of the amoA and nxrB genes among treatments and between the two stages. The abundance of the amoA gene was higher in the control group than in the carton-added treatments at the ends of both stages. This study provides an important theoretical basis for the selection of efficient ammonia nitrogen control strategies in aquaculture systems.

Assimilable organic carbon cycling within drinking water distribution systems

A new conceptual model to describe and understand the role of assimilable organic carbon (AOC) within drinking water distribution systems is proposed. The impact of AOC on both drinking water biofilm and water quality was studied using bespoke pipe loop experimental facilities installed at three carefully selected operational water treatment works. Integrated physical, chemical and biological monitoring was undertaken that highlights the central role of biofilms in AOC cycling, forming the basis of the new conceptual model. Biofilms formed under high AOC conditions were found to pose the highest discoloration response, generating a turbidity (4.3 NTU) and iron (241.5 µg/l) response sufficient to have caused regulatory failures from only 20 m of pipe in only 12 months of operation. This new knowledge of the role of biofilms in AOC cycling, and ultimately impacts on water quality, can be used to inform management and help ensure the supply of high-quality, biostable drinking water.

Simultaneous Carbon and Nitrogen Removal from Domestic Wastewater using High Rate Vermifilter

Being a cost-effective and environmentally benign technology, vermifiltration has significantly replaced the available conventional wastewater remediation methods in many cases over the last few decades. The present work emphasizes on the investigation of the nitrogen transformation dynamics, in addition to the organic carbon abatement in the designed high rate hybrid vermifilter. Moreover, the economical sustainability of the vermifiltration technology has also been enlightened by creating a bridge with the concept of circular bio-economy. The designed high rate macrophyte-assisted vermifilter (MAVF) ascertained significant high nitrogen and organic carbon removal efficiencies from the real domestic sewage, considering the chemical oxygen demand (COD) of the influent and hydraulic loading rate (HLR) as the input variables. The designed MAVF facilitated the maximum ammonium nitrogen (NH4 +-N), organic nitrogen, and total kjeldahl nitrogen removal efficiencies up to 98.2 ± 0.70%, 100%, and 99 ± 0.47%, respectively when COD of the influent and HLR were 200 ± 25 mg/L and 3 ± 0.1 m3/m2-d, respectively. On the other hand, substantial enhancement in the nitrate nitrogen (NO3 --N) in the effluent (73 ± 10.55 times its influent concentration) was observed with influent COD of 200 ± 25 mg/L and HLR of 7 ± 0.2 m3/m2-d. When the influent COD and HLR were maintained at 700 ± 45 mg/L and 3 ± 0.1 m3/m2-d, respectively, the highest total nitrogen removal of 87 ± 2.25% was obtained. Alternatively, the influent COD of 200 ± 25 mg/L and HLR of 3 ± 0.1 m3/m2-d yielded the highest COD removal efficiency of 77 ± 1.59%. Hence, the outcome of the present research work strengthens the suitability of the vermifiltration technology as an economically and ecologically sound natural wastewater bio-remediation technology for the treatment of domestic wastewater.

Insight into how high dissolved oxygen favors the startup of nitritation with aerobic granules

To elucidate how high dissolved oxygen (DO) favors the startup of nitritation with aerobic granular sludge, two granular reactors were operated under low (1-2 mg O₂·L^-1) and high DO (3-5 mg O₂·L^-1) conditions with similar effluent ammonium concentrations (>20 mg N·L^-1). The results showed that though nitritation with an average nitrite accumulation ratio of above 95% was finally achieved in both reactors, a five-fold start-up time (eleven weeks) was required for the low DO reactor compared to the high DO reactor. Moreover, the nitritation performance was positively correlated with the extent of nitrifiers stratification in granules. The faster startup of nitritation under high DO conditions mainly resulted from the faster formation of well-stratified nitrifiers, with ammonium oxidizing bacteria (AOB) dominating granule surface. High DO operation combined with sufficient ammonium supply ensured the faster growth of AOB, which should provide a competitive advantage to AOB in competing for habitable space (i.e., granule surface). Besides, the lower porosity, larger size, and more active extracellular polymeric substances (particularly proteins) production of granules was observed under the high DO condition. Overall, these findings supported the proposition that the switch from mixed to stratified distribution of nitrifiers in granule was primarily driven by their competition for habitable space rather than by oxygen-limitation.

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (K_{m(app)_NH3} ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (K_{m(app)_NO2}- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.

Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant

Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the amoA genes of ammonia-oxidizing bacteria and archaea (AOB and AOA) and a complete ammonia oxidizer (comammox) in the biofilm formed on the carriers in a full-scale WWTP. The quantification of amoA genes showed that the abundance of AOB and comammox was markedly greater in the biofilm than in the activated sludge suspended in a tank solution of the WWTP, while AOA was not detected in the biofilm or the activated sludge. A phylogenetic analysis of amoA genes revealed that as-yet-uncultivated comammox Nitrospira and uncultured AOB Nitrosomonas were predominant in the biofilm. The present results suggest that the biofilm formed on the surface of carriers enable comammox Nitrospira and AOB Nitrosomonas to co-exist and remain in the full-scale WWTP tank surveyed in this study.

Fast start-up strategies of MBBR for mariculture wastewater treatment

Moving bed biofilm reactor (MBBR) is widely used for ammonia removal in saline recirculating aquaculture systems but often faces a slow start-up problem. The aim of this study was to develop a strategy for the rapid start-up of MBBR treating synthetic mariculture wastewater. Changes in nitrification performance, biofilm characteristics and bacterial community were assessed in response to various start-up strategies: R1 as the control; R2 with step-decrease of inlet NH₄⁺-N; R3 with step-increase of inlet salinity; R4 added with particulate organic matter (POM) and R5 inoculated with nitrifying bacteria. Results show that nitrification was completed on day 63 for R3, 16-18 days faster than the other strategies. The highest protein (28.2 ± 5.1 mg/g·VS) and polysaccharide (59.4 ± 0.4 mg/g·VS) contents were observed in R3, likely linked to the faster biofilm formation. Fourier Transform infrared spectroscopy (FTIR) analysis confirmed the typical constituents of carbohydrates, proteins, lipids and DNA in biofilms. Moreover, along with the biofilm development in R3, the intensity of the peak at 1400 cm^-1 (assigned to specific amides) decreased. Pyrosequencing of 16s rRNA revealed that Gammaproteobacteria was the predominating microbial community at class level (35.6%) in R3. qPCR analysis further verified the significantly higher gene copies of amoA (1.57 × 10⁴ copies/μL) and nxrB (5.51 × 10³ copies/μL) in R3. Results obtained make the elevated salinity strategy a promising alternative for the rapid nitrification start-up of saline wastewater.

Metatranscriptomic Investigation of Adaptation in NO and N2O Production From a Lab-Scale Nitrification Process Upon Repeated Exposure to Anoxic-Aerobic Cycling

The molecular mechanisms of microbial adaptation to repeated anoxic-aerobic cycling were investigated by integrating whole community gene expression (metatranscriptomics) and physiological responses, including the production of nitric (NO) and nitrous (N2O) oxides. Anoxic-aerobic cycling was imposed for 17 days in a lab-scale full-nitrification mixed culture system. Prior to cycling, NO and N2O levels were sustained at 0.097 ± 0.006 and 0.054 ± 0.019 ppmv, respectively. Once the anoxic-aerobic cycling was initiated, peak emissions were highest on the first day (9.8 and 1.3 ppmv, respectively). By the end of day 17, NO production returned to pre-cycling levels (a peak of 0.12 ± 0.007 ppmv), while N2O production reached a new baseline (a peak of 0.32 ± 0.05 ppmv), one order of magnitude higher than steady-state conditions. Concurrently, post-cycling transcription of norBQ and nosZ returned to pre-cycling levels after an initial 5.7- and 9.5-fold increase, while nirK remained significantly expressed (1.6-fold) for the duration of and after cycling conditions. The imbalance in nirK and nosZ mRNA abundance coupled with continuous conversion of NO to N2O might explain the elevated post-cycling baseline for N2O. Metatranscriptomic investigation notably indicated possible NO production by NOB under anoxic-aerobic cycling through a significant increase in nirK expression. Opposing effects on AOB (down-regulation) and NOB (up-regulation) CO2 fixation were observed, suggesting that nitrifying bacteria are differently impacted by anoxic-aerobic cycling. Genes encoding the terminal oxidase of the electron transport chain (ccoNP, coxBC) were the most significantly transcribed, highlighting a hitherto unexplored pathway to manage high electron fluxes resulting from increased ammonia oxidation rates, and leading to overall, increased NO and N2O production. In sum, this study identified underlying metabolic processes and mechanisms contributing to NO and N2O production through a systems-level interrogation, which revealed the differential ability of specific microbial groups to adapt to sustained operational conditions in engineered biological nitrogen removal processes.

Impact of cell cluster size on apparent half-saturation coefficients for oxygen in nitrifying sludge and biofilms

A three-dimensional (3-D) diffusion-reaction model was used to assess the effects of nitrifiers growing in cell clusters on the apparent oxygen half-saturation coefficients in activated sludge flocs. The model allows conciliation of seemingly contradictory reports by several research groups. Although intrinsic half-saturation coefficients (i.e., not affected by diffusion) show a better affinity for oxygen for ammonia oxidizing (AOB) than for nitrite oxidizing bacteria (NOB) (K_O,AOB < K_O,NOB), measurements in flocs often produced reversed apparent values (K_O,AOB,app > K_O,NOB,app), which can now be explained by the 3-D model with AOB and NOB microcolonies. This effect cannot be described with a conventional 1-D homogeneous model because the reversion of the AOB/NOB apparent K_O is caused by the high biomass density and resulting concentration gradients inside the microcolonies. Two main factors explain the reversion of the half-saturation coefficients: the difference in oxygen yields (for NOB lower than for AOB) and the difference in colony size (NOB colonies are smaller than those of AOB). The strongest increase in the apparent half-saturation coefficients is linked to the colony size, rather than to the floc size. For high-density microbial aggregates (i.e., granular sludge), the need for a stratified population (AOB outer shell, NOB inner layers) was revealed in order to outcompete NOB. This study stresses the need for a more detailed description of the biomass distribution in activated sludge, granular sludge and biofilm reactors when elucidating the mechanisms for NOB repression.

A New Acyl-homoserine Lactone Molecule Generated by Nitrobacter winogradskyi

It is crucial to reveal the regulatory mechanism of nitrification to understand nitrogen conversion in agricultural systems and wastewater treatment. In this study, the nwiI gene of Nitrobacter winogradskyi was confirmed to be a homoserine lactone synthase by heterologous expression in Escherichia coli that synthesized several acyl-homoserine lactone signals with 7 to 11 carbon acyl groups. A novel signal, 7, 8-trans-N-(decanoyl) homoserine lactone (C10:1-HSL), was identified in both N. winogradskyi and the recombined E. coli. Furthermore, this novel signal also triggered variances in the nitrification rate and the level of transcripts for the genes involved in the nitrification process. These results indicate that quorum sensing may have a potential role in regulating nitrogen metabolism.

Performance and influence factors of completely autotrophic nitrogen removal over nitrite (CANON) process in a biofilter packed with volcanic rocks

Completely autotrophic nitrogen removal over nitrite (CANON) process was considered as one of the most efficient and economical nitrogen removal processes, which was suitable for treating wastewater with low ratio of carbon to nitrogen. In this study, an enlarging start-up strategy for CANON process was proposed, and a 40-L CANON reactor was successfully started by seeding 2-L mature biofilm containing both aerobic ammonia-oxidizing bacteria (AerAOB) and anaerobic ammonia-oxidizing bacteria (AnAOB). The effects of dissolved oxygen (DO), ammonia loading rate and the ratio of air inflow to water inflow (Qair/Qwater) on nitrogen removal performance were investigated. The distribution of AerAOB and AnAOB was analysed using fluorescence in situ hybridization (FISH) technique. The system reached a maximum NRR of 3.11 kg N m(-3) d(-1) with a removal efficiency of 89.5%, and the average value in steady state was 2.42±0.26 and (83.07 ± 6.89)%, respectively. Analysis of influence factors showed the important role of high DO (around 5 mg L(-1)), for the high-rate nitrogen removal, and the Qair/Qwater should be controlled at 28-40 for stable operation. FISH results suggested that AerAOB and AnAOB predominated in the reactor, with proportions of 46.8% and 39.3%, respectively. This study demonstrated that the biofilter operated with high effluent DO was a feasible setup for CANON process.

Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea

The ammonia-oxidizing archaeon Nitrosopumilus maritimus strain SCM1 (strain SCM1), a representative of the Thaumarchaeota archaeal phylum, can sustain high specific rates of ammonia oxidation at ammonia concentrations too low to sustain metabolism by ammonia-oxidizing bacteria (AOB). One structural and biochemical difference between N. maritimus and AOB that might be related to the oligotrophic adaptation of strain SCM1 is the cell surface. A proteinaceous surface layer (S-layer) comprises the outermost boundary of the strain SCM1 cell envelope, as opposed to the lipopolysaccharide coat of Gram-negative AOB. In this work, we compared the surface reactivities of two archaea having an S-layer (strain SCM1 and Sulfolobus acidocaldarius) with those of four representative AOB (Nitrosospira briensis, Nitrosomonas europaea, Nitrosolobus multiformis, and Nitrosococcus oceani) using potentiometric and calorimetric titrations to evaluate differences in proton-ionizable surface sites. Strain SCM1 and S. acidocaldarius have a wider range of proton buffering (approximately pH 10-3.5) than the AOB (approximately pH 10-4), under the conditions investigated. Thermodynamic parameters describing proton-ionizable sites (acidity constants, enthalpies, and entropies of protonation) are consistent with these archaea having proton-ionizable amino acid side chains containing carboxyl, imidazole, thiol, hydroxyl, and amine functional groups. Phosphorous-bearing acidic functional groups, which might also be present, could be masked by imidazole and thiol functional groups. Parameters for the AOB are consistent with surface structures containing anionic oxygen ligands (carboxyl- and phosphorous-bearing acidic functional groups), thiols, and amines. In addition, our results showed that strain SCM1 has more reactive surface sites than the AOB and a high concentration of sites consistent with aspartic and/or glutamic acid. Because these alternative boundary layers mediate interaction with the local external environment, these data provide the basis for further comparisons of the thermodynamic behavior of surface reactivity toward essential nutrients.

Autotrophic nitrogen removal from domestic sewage in MBR-CANON system and the biodiversity of functional microbes

The feasibility of completely autotrophic nitrogen removal over nitrite (CANON) process for treating domestic sewage was investigated in membrane bioreactor (MBR), for which conventional activated sludge was seeded at ambient temperature. By gradually decreasing hydraulic retention time under the oxygen-limited condition, CANON was successfully started-up for 78 days. Finally the MBR-CANON system was adopted for treating domestic sewage, nitrogen and COD removal achieved to 0.97 kg m(-3) d(-1), 80%, respectively, with the effluent turbidity below 1.0 NTU. DGGE profiles showed a distinct community shift of the functional bacteria after seeded to the reactor, and phylogenetic results indicated the predominance of Nitrosomonas and Candidatus Kuenenia stuttgartiensis for nitrogen removal in the reactor. FISH results showed the predominance of aerobic ammonia oxidizing bacteria (AerAOB) and anaerobic ammonia oxidizing bacteria (AnAOB) in the system, both of whose proportion reduced when treated domestic sewage.

An N-acyl homoserine lactone synthase in the ammonia-oxidizing bacterium Nitrosospira multiformis

The chemolithoautotrophic bacterium Nitrosospira multiformis is involved in affecting the process of nitrogen cycling. Here we report the existence and characterization of a functional quorum sensing signal synthase in N. multiformis. One gene (nmuI) playing a role in generating a protein with high levels of similarity to N-acyl homoserine lactone (AHL) synthase protein families was identified. Two AHLs (C14-AHL and 3-oxo-C14-AHL) were detected using an AHL biosensor and liquid chromatography-mass spectrometry (LC-MS) when nmuI, producing a LuxI homologue, was introduced into Escherichia coli. However, by extracting N. multiformis culture supernatants with acidified ethyl acetate, no AHL product was obtained that was capable of activating the biosensor or being detected by LC-MS. According to reverse transcription-PCR, the nmuI gene is transcribed in N. multiformis, and a LuxR homolog (NmuR) in this ammonia-oxidizing strain showed great sensitivity to long-chain AHL signals by solubility assay. A degradation experiment demonstrated that the absence of AHL signals might be attributed to the possible AHL-inactivating activities of this strain. To summarize, an AHL synthase gene (nmuI) acting as a long-chain AHL producer has been found in a chemolithotrophic ammonia-oxidizing microorganism, and the results provide an opportunity to complete the knowledge of the regulatory networks in N. multiformis.

Performance and microbial community of completely autotrophic nitrogen removal over nitrite (CANON) process in two membrane bioreactors (MBR) fed with different substrate levels

To study the influence of substrate on completely autotrophic nitrogen removal over nitrite (CANON) process, two membrane bioreactors (MBR) with identical setup but fed with different substrate levels (R1 with low ammonia, R2 with high ammonia), were adopted in this study. The nitrogen removal performance, bioactivity, biodiversity and distribution of the functional microorganisms in two reactors were investigated. Both the aerobic ammonia-oxidizing bacteria (AerAOB) and anaerobic ammonia-oxidizing bacteria (AnAOB) in R2 showed higher bioactivity than those in R1, while nitrite-oxidizing bacteria (NOB) showed the contrary result. Nitrosomonas and Candidatus Kuenenia stuttgartiensis were detected as predominant functional microbes in the two reactors while Nitrobacter only existed in R1. High influent ammonia possibly led to the higher biodiversity of AerAOB and the more densely packed distribution. Meanwhile, this study has demonstrated the feasibility of increasing ammonia for rapid start-up, and decreasing HRT for high-rate nitrogen removal in CANON process.

Assessment of bacterial and structural dynamics in aerobic granular biofilms

Aerobic granular sludge (AGS) is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors (SBR) fed with synthetic wastewater, namely a bubble column (BC-SBR) operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR) and Competibacter (GAO-SBR) operated at steady-state. In the BC-SBR, granules formed within 2 weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37-79%) led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80-100%), nitrogen removal (43-83%), and high but unstable dephosphatation (75-100%) were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5%) were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56 ± 10%) that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37 ± 11%). Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant population involved.

Distribution and genetic diversity of functional microorganisms in different CANON reactors

Completely autotrophic nitrogen removal over nitrite (CANON) has been regarded as an efficient and economical process for nitrogen removal from wastewater. The distribution and genetic diversity of the functional microorganisms in five lab-scale CANON reactors have been investigated by using some molecular biology methods. Nitrosomonas-like aerobic ammonium oxidizing bacteria (AerAOB) and Candidatus Brocadia-related anaerobic ammonium oxidizing bacteria (AnAOB) were detected as predominant functional microbes in the five reactors while Nitrobacter-like nitrite oxidizing bacteria (NOB) existed only in the systems operated at ambient temperature. Communities of AerAOB and AnAOB were almost similar among the five reactors while the distribution of the functional microbes was either scattered or densely packed. Meanwhile, this study has demonstrated the feasibility of starting up CANON by inoculating conventional activated sludge in low ammonium content at ambient temperature.

Nitrification and microbiological evolution during aerobic treatment of municipal solid wastes

Nitrification is a key step in the nitrogen cycle in various ecosystems. In this study, the nitrogen dynamic and the evolution of groups of microorganisms were studied during aerobic treatment of fine organic fraction of municipal solid wastes. Mineralization of organic nitrogen exhibited two phases and resulted in two ammonia emissions peaks. The nitrogen balance indicated the onset of nitrification only during the maturation stage, which was confirmed by the accumulations of both nitrite and nitrate and the nitrous oxide emissions in this period. A significant development of ammonia-oxidizing bacteria correlated to the onset of nitrification. On the contrary, ammonia-oxidizing archaea were less abundant and declined through treatment. Identification of these ammonia oxidizers indicates that the Nitrosomonas europaea/eutropha-like ammonia oxidizing bacteria were responsible for ammonia oxidation instead of other groups of ammonia oxidizers during aerobic treatment of fine organic fraction of municipal solid wastes.

N2O emission from a partial nitrification-anammox process and identification of a key biological process of N2O emission from anammox granules

Emission of nitrous oxide (N(2)O) during biological wastewater treatment is of growing concern. The emission of N(2)O from a lab-scale two-reactor partial nitrification (PN)-anammox reactor was therefore determined in this study. The average emission of N(2)O from the PN and anammox process was 4.0±1.5% (9.6±3.2% of the removed nitrogen) and 0.1±0.07% (0.14±0.09% of the removed nitrogen) of the incoming nitrogen load, respectively. Thus, a larger part (97.5%) of N(2)O was emitted from the PN reactor. The total amount of N(2)O emission from the PN reactor was correlated to nitrite (NO(2)(-)) concentration in the PN effluent rather than DO concentration. In addition, further studies were performed to indentify a key biological process that is responsible for N(2)O emission from the anammox process (i.e., granules). In order to characterize N(2)O emission from the anammox granules, the in situ N(2)O production rate was determined by using microelectrodes for the first time, which was related to the spatial organization of microbial community of the granule as determined by fluorescence in situ hybridization (FISH). Microelectrode measurement revealed that the active N(2)O production zone was located in the inner part of the anammox granule, whereas the active ammonium consumption zone was located above the N(2)O production zone. Anammox bacteria were present throughout the granule, whereas ammonium-oxidizing bacteria (AOB) were restricted to only the granule surface. In addition, addition of penicillin G that inhibits most of the heterotrophic denitrifiers and AOB completely inhibited N(2)O production in batch experiments. Based on these results obtained, denitrification by putative heterotrophic denitrifiers present in the inner part of the granule was considered the most probable cause of N(2)O emission from the anammox reactor (i.e., granules).

A great leap forward in microbial ecology

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

Inoculum effects on community composition and nitritation performance of autotrophic nitrifying biofilm reactors with counter-diffusion geometry

The link between nitritation success in a membrane-aerated biofilm reactor (MABR) and the composition of the initial ammonia- and nitrite-oxidizing bacterial (AOB and NOB) population was investigated. Four identically operated flat-sheet type MABRs were initiated with two different inocula: from an autotrophic nitrifying bioreactor (Inoculum A) or from a municipal wastewater treatment plant (Inoculum B). Higher nitritation efficiencies (NO(2)(-)-N/NH(4)(+)-N) were obtained in the Inoculum B- (55.2-56.4%) versus the Inoculum A- (20.2-22.1%) initiated reactors. The biofilms had similar oxygen penetration depths (100-150 µm), but the AOB profiles [based on 16S rRNA gene targeted real-time quantitative PCR (qPCR)] revealed different peak densities at or distant from the membrane surface in the Inoculum B- versus A-initiated reactors, respectively. Quantitative fluorescence in situ hybridization (FISH) revealed that the predominant AOB in the Inoculum A- and B-initiated reactors were Nitrosospira spp. (48.9-61.2%) versus halophilic and halotolerant Nitrosomonas spp. (54.8-63.7%), respectively. The latter biofilm displayed a higher specific AOB activity than the former biofilm (1.65 fmol cell(-1) h(-1) versus 0.79 fmol cell(-1) h(-1) ). These observations suggest that the AOB and NOB population compositions of the inoculum may determine dominant AOB in the MABR biofilm, which in turn affects the degree of attainable nitritation in an MABR.

Nitrogen removal from digested black water by one-stage partial nitritation and anammox

This study assessed the technical feasibility to treat digested black water from vacuum toilets (> 1000 mg NH4(+)-N L(-1)) in a lab-scale oxygen-limited autotrophic nitrification/denitrification (OLAND) rotating biological contactor. After an adaptation period of 2.5 months, a stable nitrogen removal rate of ca. 700 mg N L(-1) d(-1) was reached over the subsequent 5 months. Suppression of the nitrite oxidizing bacteria at free ammonia levels above 3 mg N L(-1) resulted in a nitrogen removal efficiency of 76%. The favorable ratios of both organic and inorganic carbon to nitrogen guaranteed endured anammox activity and sufficient buffering capacity, respectively. Quantitative FISH showed that aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB) made up 43 and 8% of the biofilm, respectively. Since a part of the AerAOB was probably present in anoxic biofilm zones; their specific ammonium conversion was very low, in contrast to the high specific AnAOB activity. DGGE analysis showed that the dominant AerAOB and AnAOB species were resistant to the transition from synthetic medium to digested black water. This study demonstrates high-rate nitrogen removal from digested black water by one-stage partial nitritation and anammox, which will allow a significant decrease in operational costs compared to conventional nitrification/ denitrification.

Innovative solid-state microelectrode for nitrite determination in a nitrifying granule

Nitrite is an intermediate of both nitrification and denitrification in biological removal of nitrogen from wastewater, and in situ measurement of nitrite concentration in a biofilm or microbial granules is highly desirable. However, a solid-state microelectrode for nitrite determination is not available yet In this work, a solid-state microelectrode was manufactured through electrochemical codeposition of Pt--Fe nanoparticles on a gold microelectrode fabricated using photolithography for in situ nitrite determination. This gold-based microelectrode could be used as a more cost-effective, efficient, and reliable alternative to the liquid membrane microelectrode. Nanoparticles with an average diameter of 50 nm were observed on the surface of the chemically modified electrode. A sigmoid peak at ca. 0.7 V (vs Ag/AgCl) was found on the linear sweep voltammogram in nitrite solutions by using the fabricated microelectrode. The peak height of the first-order derivative of the sigmoid peak was proportional to the nitrite concentration of 0.001--0.05 M and could be used for quantitative determination of nitrite. The detection limits (S/N = 3) were approximately 3 x 10(-5) M. The nitrite microprofiles of aerobic granules from a nitrifying reactor were measured with the microelectrode to demonstrate its potential applications with high spatial resolution.

Nitrifying genera in activated sludge may influence nitrification rates

Sequencing batch reactors were acclimated under aerobic and alternating anoxic/aerobic conditions. Greater nitrification rates in the alternating reactor were investigated by comparing environmental conditions. In the alternating reactor, pH, alkalinity, oxygen, and nitrite were higher at the onset of aerobic nitrification. Kinetic studies and batch tests, with biomass developed under aerobic and alternating conditions, revealed that these factors were insufficient to explain the divergent nitrification rates. Nitrifying genera vary in nitrification kinetics and sensitivity to environmental conditions. Nitrosospira and Nitrospira spp. could dominate in aerobic reactors, as they are adapted to low nitrite and oxygen conditions. Nitrosomonas and Nitrobacter spp. are better competitors with abundant substrates and have higher nitrite tolerance, so they could excel under alternating conditions. This theoretical explanation is consistent with the kinetics and environmental conditions in these reactors and argues for using alternating treatment, because the harsh conditions select for populations with inherently faster nitrification rates.

Activated sludge operational regime has significant impact on the type of nitrifying community and its nitrification rates

A nitrifying sequencing batch reactor, operated under alternating anoxic/aerobic conditions achieved twice the nitrification rates of its strictly aerobic counterpart. Microbial populations in both reactors were examined with fluorescent in situ hybridization (FISH) and kinetic batch studies to determine the effects of ammonium, nitrite, and oxygen. FISH revealed a dominance of rapid nitrifiers like Nitrosomonas and Nitrobacter (79.5% of the nitrifying population) in the alternating reactor, compared with the dominance of slower nitrifiers like Nitrosospira and Nitrospira (78.2%) in the strictly aerobic reactor. Nitrifiers in the aerobic reactor operated at maximum rates and were negatively affected by ammonium or nitrite, whereas nitrifying rates in the alternating reactor were proportional to ammonium or nitrite concentrations. The alternating conditions were more favorable because they selected for faster nitrifiers due to their oxidation, growth, and decay rates. The findings are of importance to the design engineers, as the reactors are typically designed based on nitrifiers' growth rate determined in strictly aerobic conditions.

Biological removal of nitrogen from wastewater

This comprehensive review discusses diverse conventional and novel technologies for nitrogen removal from wastewater. Novel technologies have distinct advantages in terms of saving configuration, aeration, and carbon sources. Each novel technology possesses promising features and potential problems. For instance, SND and OLAND processes can achieve 100% total nitrogen removal, but the low oxygen concentration required by these two processes substantially reduces the nitrification rate, which limits their application. On the other hand, denitrification can still be carried out by aerobic denitrifiers at high DO levels in activated sludge process, but it is difficult to cultivate this type of bacteria. The SHARON process is most commonly used for shortcut nitrification and denitrification because of its low requirements for retention time, oxygen concentration, and carbon source. However, its high operational temperature (about 35 degrees C) limits the application. Several real-time control strategies (DO, pH, and ORP) have been developed to achieve a stable nitrite accumulation in SHARON. The ANAMMOX process can sustain at high total-N loadings and has been employed in full-scale treatment plants, but the problem of nitrite supply has not been solved, and the treated wastewater still contains nitrate. In addition, the inoculation and enrichment of ANAMMOX bacteria (i.e., anaerobic AOB) is difficult. The problem of nitrite supply has been solved by combining partial nitrification with ANAMMOX, which provides abundant nitrite for anaerobic AOB. ANAMMOX is currently used for treating sludge digestion supernatant. Aerobic dammonitrification is a process combining partial nitrification and ANAMMOX at different layers of biofilm. Although the technology has been tested in pilot- and full-scale experiments, the mechanism is still unclear. CANON and OLAND are one-step ammonium removal processes that possess distinct advantages of saving carbon sources and aeration costs. The major challenge is the enrichment of anaerobic microorganisms capable of oxidizing ammonia with nitrite as the electron acceptor. Molecular biology and environmental biotechnology can help identify functional microorganisms, characterize microbial communities, and develop new nitrogen removal processes. Extensive research should be conducted to apply and optimize these novel processes in wastewater treatment plants. More effort should be invested to combine these novel processes (e.g., partial nitrification, ANAMMOX) to enhance nitrogen removal efficiency.

Influence of detachment on substrate removal and microbial ecology in a heterotrophic/autotrophic biofilm

Competition between heterotrophic bacteria oxidizing organic substrate and autotrophic nitrifying bacteria in a biofilm was evaluated. The biofilm was grown in a tubular reactor under different shear and organic substrate loading conditions. The reactor was initially operated without organic substrate in the influent until stable ammonia oxidation rates of 2.1 gN/(m(2)d) were achieved. A rapid increase of fluid shear in the tubular reactor on day 156 resulted in biofilm sloughing, reducing the biofilm thickness from 330 to 190 microm. This sloughing event did not have a significant effect on ammonia oxidation rates. The addition of acetate to the influent of the reactor resulted in decreased ammonia oxidation rates (1.8 gN/(m(2)d)) for low influent acetate concentrations (17 mg COD/L) and the breakdown of nitrification at high influent acetate concentrations (55 mg COD/L). Rapidly increasing fluid shear triggered biofilm sloughing in some cases--but maintaining constant shear did not prevent sloughing events from occurring. With the addition of acetate to the influent of the reactor, the biofilm thickness increased up to 1350 microm and individual sloughing events removed up to 50% of the biofilm. Biofilm sloughing had no significant influence on organic substrate removal or ammonia oxidation. During 325 days of reactor operation, ammonia was oxidized only to nitrite; no nitrate production was observed. This lack of nitrite oxidation was confirmed by fluorescent in situ hybridization (FISH) analysis, which detected betaproteobacterial ammonia oxidizers but not nitrite oxidizers. Mathematical modeling correctly predicted breakdown of nitrification at high influent acetate concentrations. Model predictions deviated systematically from experimental results, however, for the case of low influent acetate concentrations.

A computational model for biofilm-based microbial fuel cells

This study describes and evaluates a computational model for microbial fuel cells (MFCs) based on redox mediators with several populations of suspended and attached biofilm microorganisms, and multiple dissolved chemical species. A number of biological, chemical and electrochemical reactions can occur in the bulk liquid, in the biofilm and at the electrode surface. The evolution in time of important MFC parameters (current, charge, voltage and power production, consumption of substrates, suspended and attached biomass growth) has been simulated under several operational conditions. Model calculations evaluated the effect of different substrate utilization yields, standard potential of the redox mediator, ratio of suspended to biofilm cells, initial substrate and mediator concentrations, mediator diffusivity, mass transfer boundary layer, external load resistance, endogenous metabolism, repeated substrate additions and competition between different microbial groups in the biofilm. Two- and three-dimensional model simulations revealed the heterogeneous current distribution over the planar anode surface for younger and patchy biofilms, but becoming uniform in older and more homogeneous biofilms. For uniformly flat biofilms one-dimensional models should give sufficiently accurate descriptions of produced currents. Voltage- and power-current characteristics can also be calculated at different moments in time to evaluate the limiting regime in which the MFC operates. Finally, the model predictions are tested with previously reported experimental data obtained in a batch MFC with a Geobacter biofilm fed with acetate. The potential of the general modeling framework presented here is in the understanding and design of more complex cases of wastewater-fed microbial fuel cells.

In situ activity and spatial organization of anaerobic ammonium-oxidizing (anammox) bacteria in biofilms

We investigated autotrophic anaerobic ammonium-oxidizing (anammox) biofilms for their spatial organization, community composition, and in situ activities by using molecular biological techniques combined with microelectrodes. Results of phylogenetic analysis and fluorescence in situ hybridization (FISH) revealed that "Brocadia"-like anammox bacteria that hybridized with the Amx820 probe dominated, with 60 to 92% of total bacteria in the upper part (<1,000 microm) of the biofilm, where high anammox activity was mainly detected with microelectrodes. The relative abundance of anammox bacteria decreased along the flow direction of the reactor. FISH results also indicated that Nitrosomonas-, Nitrosospira-, and Nitrosococcus-like aerobic ammonia-oxidizing bacteria (AOB) and Nitrospira-like nitrite-oxidizing bacteria (NOB) coexisted with anammox bacteria and accounted for 13 to 21% of total bacteria in the biofilms. Microelectrode measurements at three points along the anammox reactor revealed that the NH(4)(+) and NO(2)(-) consumption rates decreased from 0.68 and 0.64 micromol cm(-2) h(-1) at P2 (the second port, 170 mm from the inlet port) to 0.30 and 0.35 micromol cm(-2) h(-1) at P3 (the third port, 205 mm from the inlet port), respectively. No anammox activity was detected at P4 (the fourth port, 240 mm from the inlet port), even though sufficient amounts of NH(4)(+) and NO(2)(-) and a high abundance of anammox bacteria were still present. This result could be explained by the inhibitory effect of organic compounds derived from biomass decay and/or produced by anammox and coexisting bacteria in the upper parts of the biofilm and in the upstream part of the reactor. The anammox activities in the biofilm determined by microelectrodes reflected the overall reactor performance. The several groups of aerobic AOB lineages, Nitrospira-like NOB, and Betaproteobacteria coexisting in the anammox biofilm might consume a trace amount of O(2) or organic compounds, which consequently established suitable microenvironments for anammox bacteria.

Characterization and performance of constructed nitrifying biofilms during nitrogen bioremediation of a wastewater effluent

Constructed ammonium oxidizing biofilms (CAOB) and constructed nitrite oxidizing biofilms (CNOB) were characterized during the bioremediation of a wastewater effluent. The maximum ammonium removal rate and removal efficiency in CAOB was 322 mg N-NH4+ m(-3) d(-1) and 96%, respectively, while in CNOB a maximum removal rate of 255 mg N-NH4+ m(-3) d(-1) and a removal efficiency of 76% was achieved. Both constructed biofilms on low-density polyester Dacron support achieved removal efficiencies higher than that of the concentrations normally present in reactors without constructed biofilms (P < 0.05). Nitrifying bacteria from the constructed biofilms cultures were typed by sequencing 16S rRNA genes that had been amplified by PCR from genomic DNA. Analysis of enrichment biofilms has therefore provided evidence of high removal of ammonium and the presence of Nitrosomonas eutropha, N. halophila and N. europaea in CAOB, while in CNOB Nitrobacter hamburgensis, N. winogradskyi and N. alkalicus were identified according to 16S rRNA gene sequences comparison. The biofilm reactors were nitrifying over the whole experimental period (15 days), showing a definite advantage of constructed biofilms for enhancing a high biomass concentration as evidenced by environmental electron microscopic analysis (ESEM). Our research demonstrates that low-density polyester Dacron can be effectively used for the construction of nitrifying biofilms obtaining high removal efficiencies of nitrogen in a relatively short time from municipal effluents from wastewater treatment plants. CAOB and CNOB are potentially promissory for the treatment of industrial wastewaters that otherwise requires very large and expensive reactors for efficient bioremediation of effluents.

Biological filtration limits carbon availability and affects downstream biofilm formation and community structure

Carbon removal strategies have gained popularity in the mitigation of biofouling in water reuse processes, but current biofilm-monitoring practices based on organic-carbon concentrations may not provide an accurate representation of the in situ biofilm problem. This study evaluated a submerged microtiter plate assay for direct and rapid monitoring of biofilm formation by subjecting the plates to a continuous flow of either secondary effluent (SE) or biofilter-treated secondary effluent (BF). This method was very robust, based on a high correlation (R(2) = 0.92) between the biomass (given by the A(600) in the microtiter plate assay) and the biovolume (determined from independent biofilms developed on glass slides under identical conditions) measurements, and revealed that the biomasses in BF biofilms were consistently lower than those in SE biofilms. The influence of the organic-carbon content on the biofilm community composition and succession was further evaluated using molecular tools. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed a group of pioneer colonizers, possibly represented by Sphingomonadaceae and Caulobacter organisms, to be common in both SE and BF biofilms. However, differences in organic-carbon availabilities in the two water samples eventually led to the selection of distinct biofilm communities. Alphaproteobacterial populations were confirmed by fluorescence in situ hybridization to be enriched in SE biofilms, while Betaproteobacteria were dominant in BF biofilms. Cloning analyses further demonstrated that microorganisms adapted for survival under low-substrate conditions (e.g., Aquabacterium, Caulobacter, and Legionella) were preferentially selected in the BF biofilm, suggesting that carbon limitation strategies may not achieve adequate biofouling control in the long run.

Three-dimensional biofilm model with individual cells and continuum EPS matrix

An innovative type of biofilm model is derived by combining an individual description of microbial particles with a continuum representation of the biofilm matrix. This hybrid model retains the advantages of each approach, while providing a more realistic description of the temporal development of biofilm structure in two or three spatial dimensions. The general model derivation takes into account any possible number of soluble components. These are substrates and metabolic products, which diffuse and react in the biofilm within individual microbial cells. The cells grow, divide, and produce extracellular polymeric substances (EPS) in a multispecies model setting. The EPS matrix is described by a continuum representation as incompressible viscous fluid, which can expand and retract due to generation and consumption processes. The cells move due to a pushing mechanism between cells in colonies and by an advective mechanism supported by the EPS dynamics. Detachment of both cells and EPS follows a continuum approach, whereas cells attach in discrete events. Two case studies are presented for model illustration. Biofilm consolidation is explained by shrinking due to EPS and cell degradation processes. This mechanism describes formation of a denser layer of cells in the biofilm depth and occurrence of an irregularly shaped biofilm surface under nutrient limiting conditions. Micro-colony formation is investigated by growth of autotrophic microbial colonies in an EPS matrix produced by heterotrophic cells. Size and shape of colonies of ammonia and nitrite-oxidizing bacteria (NOB) are comparatively studied in a standard biofilm and in biofilms aerated from a membrane side.

Community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms

The bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16S rRNA gene clone analysis, fluorescence in situ hybridization (FISH) and microelectrodes. These results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (IWTP). Both nitrification and denitrification occurred in the primary denitrification (PD) tank and denitrification occurred in the secondary denitrification (SD) tank. In contrast, nitrification and denitrification rates were very low in the nitrification (N) tank. 16S rRNA gene clone sequence analysis revealed that the bacteria affiliated with Alphaproteobacteria, followed by Betaproteobacteria, were numerically important microbial groups in three tanks. The many clones affiliated with Alphaproteobacteria were closely related to the denitrifying bacteria (e.g., Hyphomicrobium spp., Rhodopseudomonas palustris, and Rhodobacter spp.). In addition, Methylophilus leisingeri affiliated with Betaproteobacteria, which favorably utilized methanol, was detected only in the SD-tank to which methanol was added. Nitrosomonas europaea and Nitrosomonas marina were detected as the ammonia-oxidizing bacteria affiliated with Betaproteobacteria throughout this plant, although the dominant species of them was different among three tanks. Nitrifying bacteria were mainly detected in the upper parts of the PD-biofilm whereas their populations were low in the upper parts of the N-biofilm. The presence of denitrifying bacteria affiliated with Hyphomicrobium spp. in SD- and N-biofilms was verified by FISH analysis. Microelectrode measurements showed that the nitrifying bacteria present in the N- and PD-biofilms were active and the bacteria present in the SD-biofilm could denitrify.

Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR

Population dynamics of ammonia-oxidizing bacteria (AOB) and uncultured Nitrospira-like nitrite-oxidizing bacteria (NOB) dominated in autotrophic nitrifying biofilms were determined by using real-time quantitative polymerase chain reaction (RTQ-PCR) and fluorescence in situ hybridization (FISH). Although two quantitative techniques gave the comparable results, the RTQ-PCR assay was easier and faster than the FISH technique for quantification of both nitrifying bacteria in dense microcolony-forming nitrifying biofilms. Using this RTQ-PCR assay, we could successfully determine the maximum specific growth rate (mu = 0.021/h) of uncultured Nitrospira-like NOB in the suspended enrichment culture. The population dynamics of nitrifying bacteria in the biofilm revealed that once they formed the biofilm, the both nitrifying bacteria grew slower than in planktonic cultures. We also calculated the spatial distributions of average specific growth rates of both nitrifying bacteria in the biofilm based on the concentration profiles of NH4+, NO2-, and O2, which were determined by microelectrodes, and the double-Monod model. This simple model estimation could explain the stratified spatial distribution of AOB and Nitrospira-like NOB in the biofilm. The combination of culture-independent molecular techniques and microelectrode measurements is a very powerful approach to analyze the in situ kinetics and ecophysiology of nitrifying bacteria including uncultured Nitrospira-like NOB in complex biofilm communities.

Application of a pH-sensitive fluoroprobe (C-SNARF-4) for pH microenvironment analysis in Pseudomonas aeruginosa biofilms

An important feature of microbial biofilms is the development of four-dimensional physical and chemical gradients in space and time. There is need for novel approaches to probe these so-called microenvironments to determine their effect on biofilm-specific processes. In this study, we describe the use of seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) for pH microenvironment analysis in Pseudomonas aeruginosa biofilms. C-SNARF-4 is a fluorescent ratiometric probe that allows pH quantification independent of probe concentration and/or laser intensity. By confocal scanning laser microscopy, C-SNARF-4 revealed pH heterogeneity throughout the biofilm in both the x,y and x,z planes, with values ranging from pH 5.6 (within the biofilm) to pH 7.0 (bulk fluid). pH values were typically remarkably different than those just a few micrometers away. Although this probe has been successfully used in a number of eukaryotic systems, problems have been reported which describe spectral emission changes as a result of macromolecular interactions with the fluorophore. To assess how the biofilm environment may influence fluorescent properties of the dye, fluorescence of C-SNARF-4 was quantified via spectrofluorometry while the probe was suspended in various concentrations of representative biofilm matrix components (i.e., proteins, polysaccharides, and bacterial cells) and growth medium. Surprisingly, our data demonstrate that few changes in emission spectra occur as a result of matrix interactions below pH 7. These studies suggest that C-SNARF-4 can be used as a reliable indicator of pH microenvironments, which may help elucidate their influence on the medical and geobiological roles of natural biofilms.

Let them fly or light them up: matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry and fluorescence in situ hybridization (FISH)

This review focuses on clinical bacteriology and by and large does not cover the detection of fungi, viruses or parasites. It discusses two completely different but complementary approaches that may either supplement or replace classic culture-based bacteriology. The latter view may appear provocative in the light of the actual market penetration of molecular genetic testing in clinical bacteriology. Despite its elegance, high specificity and sensitivity, molecular genetic diagnostics has not yet reached the majority of clinical laboratories. The reasons for this are manifold: Many microbiologists and medical technologists are more familiar with classical microbiological methods than with molecular biology techniques. Culture-based methods still represent the work horse of everyday routine. The number of available FDA-approved molecular genetic tests is limited and external quality control is still under development. Finally, it appears difficult to incorporate genetic testing in the routine laboratory setting due to the limited number of samples received or the lack of appropriate resources. However, financial and time constraints, particularly in hospitals as a consequence of budget cuts and reduced length of stay, lead to a demand for significantly shorter turnaround times that cannot be met by culture-dependent diagnosis. As a consequence, smaller laboratories that do not have the technical and personal equipment required for molecular genetic amplification techniques may adopt alternative methods such as fluorescence in situ hybridization (FISH) that combines easy-to-perform molecular hybridization with microscopy, a technique familiar to every microbiologist. FISH is hence one of the technologies presented here. For large hospital or reference laboratories with a high sample volume requiring massive parallel high-throughput testing we discuss matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of nucleic acids, a technology that has evolved from the post-genome sequencing era, for high-throughput sequence variation analysis (1, 2).