Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor

Forecasting the dynamics of a complex microbial community using integrated meta-omics

Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community. We forecast the signals over the subsequent five years and use 21 extra samples collected at defined time intervals for testing and validation. Our forecasts are correct for six signals and hint on phenomena such as predation cycles. Using all the 17 forecasts and the environmental variables, we predict gene abundance and expression, with a coefficient of determination ≥0.87 for the subsequent three years. Our study demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.

Challenges and current advances in in vitro biofilm characterization

Biofilms are structured communities of bacterial cells encased in a self-produced polymeric matrix, which develop over time and exhibit temporal responses to stimuli from internal biological processes or external environmental changes. They can be detrimental, threatening public health and causing economic loss, while they also play beneficial roles in ecosystem health, biotechnology processes, and industrial settings. Biofilms express extreme heterogeneity in their physical properties and structural composition, resulting in critical challenges in understanding them comprehensively. The lack of detailed knowledge of biofilms and their phenotypes has deterred significant progress in developing strategies to control their negative impacts and take advantage of their beneficial applications. A range of in vitro models and characterization tools have been developed and used to study biofilm growth and, specifically, to investigate the impact of environmental and growth factors on their development. This review article discusses the existing knowledge of biofilm properties and explains how external factors, such as flow condition, surface, interface, and host factor, may impact biofilm growth. The limitations of current tools, techniques, and in vitro models that are currently used for biofilms are also presented.

Unique biofilm structure and mass transfer mechanisms in the foam aerated biofilm reactor (FABR)

The foam-aerated biofilm reactor (FABR) is a novel biofilm process that can simultaneously remove carbon and nitrogen from wastewater. A porous polyurethane foam sheet forms an interface between wastewater and aerated water, making it a counter-diffusional biofilm process similar to the membrane-aerated biofilm reactor (MABR). However, it is not clear how biofilm develops the foam interior, and how this impacts mass transfer and performance. This research explored biofilm development within the foam sheet and determined whether advective transport within the sheet played a significant role. Foam sheets with 2-, 4.5- and 9-mm thicknesses were explored. Oxygen, nitrate, nitrite and ammonia profiles in the sheet were measured using microsensors, and biofilm imaging studies were carried out using optical coherence tomography (OCT). On the foam's aerated side, a dense nitrifying biofilm formed. Beyond the aerobic zone, much less biomass was observed, with a high porosity foam-biofilm layer. The higher effective diffusivity within the foam for the 4- and 9-mm sheets suggested advective transport within the foam channel structures. Using an effective diffusivity factor in conventional 1-D biofilm models reproduced the measured substrate concentration profiles within the foam. Four different practical conditions were modelled. The maximum TN removal efficiency was about 70% and a nitrogen removal flux of 1.25 gN.m-2.d-1. We conclude that mass transfer resistance occurred primarily in the dense, nitrifying layer near the aerated side. The rest of the foam sheet was porous, allowing the advective mass transfer.

Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors

A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C₆-HSL, C₈-HSL, C₁₀-HSL and 3-oxo-C₁₀-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.

Influence of COD in Toxic Industrial Wastewater from a Chemical Concern on Nitrification Efficiency

COD is an arbitrary indicator of the content of organic and inorganic compounds in wastewater. The aim of this research was to determine the effect of COD of industrial wastewater on the nitrification process. This research covered wastewater from acrylonitrile and styrene-butadiene rubbers, emulsifiers, polyvinyl acetate, styrene, solvents (butyl acetate, ethyl acetate) and owipian^® (self-extinguishing polystyrene intended for expansion) production. The volume of the analyzed wastewater reflected the active sludge load in the real biological treatment system. This research was carried out by the method of short-term tests. The nitrification process was inhibited to the greatest extent by wastewater from the production of acrylonitrile (approx. 51%) and styrene-butadiene (approx. 60%) rubbers. In these wastewaters, nitrification inhibition occurred due to the high COD load and the presence of inhibitors. Four-fold dilution of the samples resulted in a two-fold reduction in the inhibition of nitrification. On the other hand, in the wastewater from the production of emulsifiers and polyvinyl acetate, a two-fold reduction in COD (to the values of 226.4 mgO₂·dm^-3 and 329.8 mgO₂·dm^-3, respectively) resulted in a significant decrease in nitrification inhibition. Wastewater from the production of styrene, solvents (butyl acetate, ethyl acetate) and owipian^® inhibited nitrification under the influence of strong inhibitors. Lowering the COD value of these wastewaters did not significantly reduce the inhibition of nitrification.

Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

The r/K selection theory and its application in biological wastewater treatment processes

Understanding the characteristics of functional organisms is the key to managing and updating biological processes for wastewater treatment. This review, for the first time, systematically characterized two typical types of strategists in wastewater treatment ecosystems via the r/K selection theory and provided novel strategies for selectively enriching microbial community. Functional organisms involved in nitrification (e.g., Nitrosomonas and Nitrosococcus), anammox (Candidatus Brocadia), and methanogenesis (Methanosarcinaceae) are identified as r-strategists with fast growth capacities and low substrate affinities. These r-strategists can achieve high pollutant removal loading rates. On the other hand, other organisms such as Nitrosospira spp., Candidatus Kuenenia, and Methanosaetaceae, are characterized as K-strategists with slow growth rates but high substrate affinities, which can decrease the pollutant concentration to low levels. More importantly, K-strategists may play crucial roles in the biodegradation of recalcitrant organic pollutants. The food-to-microorganism ratio, mass transfer, cell size, and biomass morphology are the key factors determining the selection of r-/K-strategists. These factors can be related with operating parameters (e.g., solids and hydraulic retention time), biomass morphology (biofilm or granules), and operating modes (continuous-flow or sequencing batch), etc., to achieve the efficient acclimation of targeted r-/K-strategists. For practical applications, the concept of substrate flux was put forward to further benefit the selective enrichment of r-/K-strategists, fulfilling effective management and improvement of engineered pollution control bioprocesses. Finally, the future perspectives regarding the development of the r/K selection theory in wastewater treatment processes were discussed.

In Situ Gene Expression in Native Cryofixed Bone Tissue

Bone is a very complex tissue that is constantly changing throughout the lifespan. The precise mechanism of bone regeneration remains poorly understood. Large bone defects can be caused by gunshot injury, trauma, accidents, congenital anomalies and tissue resection due to cancer. Therefore, understanding bone homeostasis and regeneration has considerable clinical and scientific importance in the development of bone therapy. Macrophages are well known innate immune cells secreting different combinations of cytokines and their role in bone regeneration during bone healing is essential. Here, we present a method to identify mRNA transcripts in cryosections of non-decalcified rat bone using in situ hybridization and hybridization chain reaction to explore gene expression in situ for better understanding the gene expression of the bone tissues.

Nitrification mainly driven by ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in an anammox-inoculated wastewater treatment system

Anaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L⁻¹ h⁻¹ and 6.52 µmol L⁻¹ h⁻¹, respectively, while the rates in sample B were 14.48 µmol L⁻¹ h⁻¹ and 14.59 µmol L⁻¹ h⁻¹, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89–4.95 × 10¹¹ copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01–9.74 × 10⁹ copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28–1.53 × 10⁵ copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.

Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata

The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community

Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.

Macrophage Identification In Situ

Understanding the processes of inflammation and tissue regeneration after injury is of great importance. For a long time, macrophages have been known to play a central role during different stages of inflammation and tissue regeneration. However, the molecular and cellular mechanisms by which they exert their effects are as yet mostly unknown. While in vitro macrophages have been characterized, recent progress in macrophage biology studies revealed that macrophages in vivo exhibited distinctive features. Actually, the precise characterization of the macrophages in vivo is essential to develop new healing treatments and can be approached via in situ analyses. Nowadays, the characterization of macrophages in situ has improved significantly using antigen surface markers and cytokine secretion identification resulting in specific patterns. This review aims for a comprehensive overview of different tools used for in situ macrophage identification, reporter genes, immunolabeling and in situ hybridization, discussing their advantages and limitations.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

The call for regional design code from the regional discrepancy of microbial communities in activated sludge

Discerning the differences in activated sludge (AS) microbial community due to geographic location and environmental and operational factors is of great significance for precise design and maintenance of wastewater treatment plants (WWTPs). Hence, in this study, 150 AS samples collected from WWTPs in South China and North China were analyzed by 16 S rRNA gene sequencing. In general, AS microbial community in North China had lower diversity, higher proportions of stochastic assembly (35.7% v.s. 15.8%) and more network keystone species (19 v.s. 5) compared with southern AS community. Conductivity and SRT had significant effects on AS community in both regions. Latitude, annual mean temperature, and influent BOD, COD, and ammonia influenced South China community significantly, while pH and influent total phosphorus affected North China community. To achieve stable performance, southern WWTPs should carefully monitor fluctuations in wastewater characteristics, while northern WWTPs should monitor AS communities for shifts in the dominant taxa from immigrant strains brought in through the influent. Additionally, WWTPs in North China should be aware of the need to proactively control sludge bulking because of the high abundance and occurrence of Haliscomenobacter in these AS communities. MAIN FINDING: The call for regional design based on the regional discrepancy of microbial communities in activated sludge is uncovered and according suggestions were given.

Simultaneous nitrification and denitrification in moving bed bioreactor and other biological systems

Moving bed bioreactor (MBBR), used for treatment of municipal and industrial wastewater, is a completely mixed attached growth type system that involves microorganisms which grow as biofilm on the surface of the suspended carriers within the reactor. If the biofilm is thick enough, dissolved oxygen in the reactor would not diffuse into deeper strata and thus anoxic/anaerobic condition develops in those regions facilitating growth of heterotrophic denitrifying bacteria. Autotrophic nitrifiers colonize the outer surface of biofilm in biocarriers as usual. Thus, development of aerobic nitrifying and anoxic denitrifying microorganisms facilitates nitrification and denitrification simultaneously within different zones of the same biofilm. The present paper summarizes the feasibility of nitrogen removal in MBBR systems via autotrophic nitrification followed by heterotrophic denitrification, including various aspects of simultaneous nitrification and denitrification (SND) process in other biofilm units as well. Apart from that, the areas for further investigation are briefly narrated from studies conducted earlier.

Critical Factors Facilitating Candidatus Nitrotoga To Be Prevalent Nitrite-Oxidizing Bacteria in Activated Sludge

Nitrite oxidation is the primary pathway that generates nitrate in engineered systems. However, little is known about the role of a novel nitrite-oxidizing bacteria (NOB) genus Candidatus Nitrotoga in activated sludge systems. To elucidate key factors that impact NOB community composition, laboratory-scale sequencing batch reactors (SBRs) were designed and operated under the same conditions as real wastewater treatment plants to achieve considerable nitrogen removal and similar community; then, different conditions including temperature (T), dissolved oxygen (DO), free nitrous acid (FNA), and free ammonia (FA) were applied. The 16S rRNA gene-based PCR and sequence analysis illustrated that Ca. Nitrotoga were abundant even at ambient temperature, thus further challenging the previous conception of them being solely cold-adapted. Ca. Nitrotoga are less competitive than Nitrospira during oxygen deficiency, indicating its lower affinity to dissolved oxygen. Ca. Nitrotoga are the dominant nitrite oxidizers under regular exposure to FNA and FA due to their relatively higher resistance than other NOB toward these two effective biocides. Therefore, this study demonstrates that Ca. Nitrotoga can play an important role in biological nitrogen removal and also highlights the need for multiple strategies for NOB suppression for the next-generation, shortcut nitrogen removal.

Nitrite production by ammonia-oxidizing bacteria mediates chloramine decay and resistance in a mixed-species community

As water distribution centres increasingly switch to using chloramine to disinfect drinking water, it is of paramount importance to determine the interactions of chloramine with potential biological contaminants, such as bacterial biofilms, that are found in these systems. For example, ammonia-oxidizing bacteria (AOB) are known to accelerate the decay of chloramine in drinking water systems, but it is also known that organic compounds can increase the chloramine demand. This study expanded upon our previously published model to compare the decay of chloramine in response to alginate, Pseudomonas aeruginosa, Nitrosomonas europaea and a mixed-species nitrifying culture, exploring the contributions of microbial by-products, heterotrophic bacteria and AOBs to chloramine decay. Furthermore, the contribution of AOBs to biofilm stability during chloramination was investigated. The results demonstrate that the biofilm matrix or extracellular polymeric substances (EPS), represented by alginate in these experiments, as well as high concentrations of dead or inactive cells, can drive chloramine decay rather than any specific biochemical activity of P. aeruginosa cells. Alginate was shown to reduce chloramine concentrations in a dose-dependent manner at an average rate of 0.003 mg l-1  h-1 per mg l-1 of alginate. Additionally, metabolically active AOBs mediated the decay of chloramine, which protected members of mixed-species biofilms from chloramine-mediated disinfection. Under these conditions, nitrite produced by AOBs directly reacted with chloramine to drive its decay. In contrast, biofilms of mixed-species communities that were dominated by heterotrophic bacteria due to either the absence of ammonia, or the addition of nitrification inhibitors and glucose, were highly sensitive to chloramine. These results suggest that mixed-species biofilms are protected by a combination of biofilm matrix-mediated inactivation of chloramine as well as the conversion of ammonia to nitrite through the activity of AOBs present in the community.

Visualizing NH3 emission and the local O2 and pH microenvironment of soil upon manure application using optical sensors

The application of fertilizers and manure on fields is the largest source of ammonia (NH₃) in the atmosphere.·NH₃ emission from agriculture has negative environmental consequences and is largely controlled by the chemical microenvironment and the respective biological activity of the soil. While gas phase and bulk measurements can describe the emission on a large scale, those measurements fail to unravel the local processes and spatial heterogeneity at the soil air interface. We report a two dimensional (2D) imaging approach capable of visualizing three of the most important chemical parameters associated with NH₃ emission from soil. Besides the released NH₃ itself also O₂ and pH microenvironments are imaged using reversible optodes in real-time with a spatial resolution of <100 µm. This combined optode approach utilizes a specifically developed NH₃ optode with a limit of detection of 2.11 ppm and a large working range (0-1800 ppm) ideally suited for studying NH₃ volatilization from soil. This NH₃ optode will contribute to a better understanding of the driving factors for NH₃ emission on a microscale and has the potential to become a valuable tool in studying NH₃ dynamics.

A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.

Performance and bacterial community structure of a novel inverse fluidized bed bioreactor (IFBBR) treating synthetic municipal wastewater

The performance of a lab-scale integrated anoxic and aerobic inverse fluidized bed bioreactors (IFBBR) for biological nutrient removal from synthetic municipal wastewater was studied at chemical oxygen demand (COD) loading rates of 0.34-2.10 kg COD/(m³-d) and nitrogen loading rates of 0.035-0.213 kg N/(m³-d). Total COD removal efficiencies of >84% were achieved, concomitantly with complete nitrification. The overall nitrogen removal efficiencies were >75%. Low biomass yields of 0.030-0.101 g VSS/g COD were achieved. Compared with other FBBR systems, the energy consumption for this IFBBR system was an average 59% less at organic loading rates (OLRs) of 1.02 and 2.10 kg COD/(m³-d). Bacterial community structures of attached and suspended biomass revealed that the dominant phyla were Proteobacteria, Bacteroidetes, and Epsilonbacteraeota, etc. The relative abundance of ammonia-oxidizing bacteria (AOBs) and nitrite-oxidizing bacteria (NOBs) in the aerobic attached biomass were 0.451% and 0.110%, respectively. COD mass balance in the anoxic zone was closed by consideration of sulfate reduction, which was confirmed by the presence of genus Chlorobium (sulfate-reducing bacteria) in the anoxic attached biofilm with a relative abundance of 0.32%.

Enhancement of nitrogen removal by supplementing fluidized-carriers into the aerobic tank in a full-scale A2/O system

Fluidized-carriers were supplemented into the aerobic tank of a full-scale wastewater treatment plant (WWTP) using an anaerobic/anoxic/aerobic (A²/O) system to improve the nitrogen removal efficiency in effluents. The effects of carrier supplementation on denitrification ability and the bacterial community structures were investigated over 10 months. The results showed that the average effluent concentration of total nitrogen (TN) was maintained at 9.46 ± 1.14 mg/L, which was lower than 15.17 ± 2.00 mg/L in the effluent without carrier supplementation, indicating that adding fluidized-carriers into the aerobic tank contributed to nitrogen removal efficiency. A thick biofilm was formed after 4 months, which provided a good anoxic-aerobic microenvironment to the microbes. Illumina sequencing analysis showed a higher bacterial diversity in the biofilm. The relative abundance of nitrifying bacteria, denitrifying bacteria, and aerobic denitrifying bacteria in the biofilms was 13.68-39%, 11.56-12.17%, and 9.76-12.50%, respectively, which was beneficial for nitrogen removal in the system. The most prevalent genera were Nitrospira, Bacillus, Thauera, Hyphomicrobium, Acinetobacter, Zoogloea, Pseudomonas, and Paracoccus, which can metabolize nitrogenous or aromatic compounds and were the major functional bacterial genera, suggesting that these organisms play key roles in biodegradation processes in the carrier-added A²/O wastewater treatment system.

Impact of ampicillin on the nitrogen removal, microbial community and enzymatic activity of activated sludge

The performance, nitrogen removal rate, extracellular polymeric substances (EPS), microbial community and enzymatic activity of activated sludge have been assessed in a sequencing batch reactor under ampicillin stress. The chemical oxygen demand and ammonia removal kept relatively stable at 0-30 mg/L ampicillin. No obvious nitrite and nitrate accumulation was found in the effluent. However, the oxygen utilization rate, nitrification rate and denitrification rate declined with the increment of ampicillin concentration. The activities of dehydrogenase and microbial enzymes relating to nitrogen removal were inhibited under ampicillin stress. Ampicillin at 20 and 30 mg/L heightened the microbial lactate dehydrogenase release and reactive oxygen species production. Ampicillin promoted the production of EPS, loosely bound EPS and tightly bound EPS and affected their chemical composition. Additionally, the protein/polysaccharide ratios in the EPS and the sludge settleability reduced with the increment of ampicillin concentration. Ampicillin obviously affected the relative abundance of nitrifying- and denitrifying bacteria.

Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action

Biofilm refers to the complex, sessile communities of microbes found either attached to a surface or buried firmly in an extracellular matrix as aggregates. The biofilm matrix surrounding bacteria makes them tolerant to harsh conditions and resistant to antibacterial treatments. Moreover, the biofilms are responsible for causing a broad range of chronic diseases and due to the emergence of antibiotic resistance in bacteria it has really become difficult to treat them with efficacy. Furthermore, the antibiotics available till date are ineffective for treating these biofilm related infections due to their higher values of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), which may result in in-vivo toxicity. Hence, it is critically important to design or screen anti-biofilm molecules that can effectively minimize and eradicate biofilm related infections. In the present article, we have highlighted the mechanism of biofilm formation with reference to different models and various methods used for biofilm detection. A major focus has been put on various anti-biofilm molecules discovered or tested till date which may include herbal active compounds, chelating agents, peptide antibiotics, lantibiotics and synthetic chemical compounds along with their structures, mechanism of action and their respective MICs, MBCs, minimum biofilm inhibitory concentrations (MBICs) as well as the half maximal inhibitory concentration (IC₅₀) values available in the literature so far. Different mode of action of anti biofilm molecules addressed here are inhibition via interference in the quorum sensing pathways, adhesion mechanism, disruption of extracellular DNA, protein, lipopolysaccharides, exopolysaccharides and secondary messengers involved in various signaling pathways. From this study, we conclude that the molecules considered here might be used to treat biofilm-associated infections after significant structural modifications, thereby investigating its effective delivery in the host. It should also be ensured that minimum effective concentration of these molecules must be capable of eradicating biofilm infections with maximum potency without posing any adverse side effects on the host.

The threshold of influent ammonium concentration for nitrate over-accumulation in a one-stage deammonification system with granular sludge without aeration

Low-strength ammonium is still a challenge for the mainstream deammonification because of nitrate over-accumulation. In this study, the threshold of influent ammonium concentration of one-stage deammonification system with granular sludge was investigated, by stepwise decreasing influent ammonium from high concentrations (280mg/L to 140mg/L) to the low concentration (70mg/L) in 108d at 32°C without aeration. Results showed that, under 70mg/L NH₄⁺-N, ΔNO₃^--N/ΔNH₄⁺-N ratio increased to 0.2, deviated from the theoretical value of 0.11, with ammonium and TN removal efficiencies of 91% and 71%, respectively. However, under both high ammonium concentrations (280mg/L and 140mg/L), nitrate production stabilized at only 13%. Chloroflexi, Planctomycetes and Proteobacteria contributed >70% of the communities under all three ammonium concentrations. As influent ammonium decreasing, the relative abundances of bacteria for anammox, aerobic oxidizing and denitrifying decreased, while NOB (nitrite oxidizing bacteria) abundance increased greatly. So 70mg/L was the threshold of influent ammonium concentration for stable deammonification without organic influent. It was the decrease of functional bacteria and overgrowth of NOB that worsen the deammonification performance under low-strength ammonium.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Effect of florfenicol on performance and microbial community of a sequencing batch biofilm reactor treating mariculture wastewater

The effects of florfenicol (FF) on the performance, microbial activity and microbial community of a sequencing batch biofilm reactor (SBBR) were evaluated in treating mariculture wastewater. The chemical oxygen demand (COD) and nitrogen removal were inhibited at high FF concentrations. The specific oxygen utilization rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) were decreased with an increase in the FF concentration from 0 to 35 mg/L. The chemical compositions of loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) could be affected with an increase in the FF concentration. The high-throughput sequencing indicated some obvious variations in the microbial community at different FF concentrations. The relative abundance of Nitrosomonas and Nitrospira showed a decreasing tendency with an increase in the FF concentration, suggesting that FF could affect the nitrification process of SBBR. Some genera capable of reducing nitrate to nitrogen gas could be inhibited by the addition of FF in the influent, such as Azospirillum and Hyphomicrobium.

Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH₄⁺ concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions.

Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.

Microbial life on a sand grain: from bulk sediment to single grains

Globally, marine surface sediments constitute a habitat for estimated 1.7 × 10²⁸ prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 10⁴-10⁵ cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)_0.97. Only 4-8 single grains are needed to cover 50% of OTU_0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.

High-rate nitrification of electronic industry wastewater by using nitrifying granules

Nitrifying granules have a high sedimentation property and an ability to maintain a large amount of nitrifying bacteria in a reaction tank. Our group has examined the formation process of nitrifying granules and achieved high-rate nitrification for an inorganic synthetic wastewater using these granules. In this research, a pilot-scale test plant with an 850-liter reaction tank was assembled in a semiconductor manufacturing factory in order to conduct a continuous water conduction test using real electronics industry wastewater. The aim was to observe the formation of nitrifying granules and determine the maximum ammonia removal rate. The average granule diameter formed during the experiment was 780 μm and the maximum ammonia removal rate was observed to be 1.5 kgN·m^-3·day^-1 at 20 °C, which is 2.5-5 times faster than traditional activated sludge methods. A fluorescence in situ hybridization analysis showed that β-proteobacterial ammonia oxidizing bacteria and the Nitrospira-like nitrite-oxidizing bacteria dominate the bacteria population in the granules, and their strong aggregation capacity might confer some benefits to the formation of these nitrifying granules.

Myriophyllum aquaticum Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater

Removal of nitrogen (N) is a critical aspect in the functioning of constructed wetlands (CWs), and the N treatment in CWs depends largely on the presence and activity of macrophytes and microorganisms. However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha^-1 d^-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA) and denitrifying genes (nirS, nirK, and nosZ) were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold) and nirS genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera), nitrite-oxidizing bacteria (Nitrospira), and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments. The results of a canonical correspondence analysis and Mantle tests indicated that M. aquaticum may shift the sediment microbial community by changing the sediment chemical properties. The enriched nitrifiers and denitrifiers were distributed widely in the vegetated sediments, showing positive ecological associations among themselves and other bacteria based on phylogenetic molecular ecological networks.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

BACKGROUND

Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations.

RESULTS

The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance.

CONCLUSIONS

Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.

Impact of microbial physiology and microbial community structure on pharmaceutical fate driven by dissolved oxygen concentration in nitrifying bioreactors

Operation at low dissolved oxygen (DO) concentrations (<1 mg/L) in wastewater treatment could save utilities significantly by reducing aeration energy costs. However, few studies have evaluated the impact of low DO on pharmaceutical biotransformations during treatment. DO concentration can impact pharmaceutical biotransformation rates during wastewater treatment both directly and indirectly: directly by acting as a limiting substrate that slows the activity of the microorganisms involved in biotransformation; and indirectly by shaping the microbial community and selecting for a community that performs pharmaceutical biotransformation faster (or slower). In this study, nitrifying bioreactors were operated at low (∼0.3 mg/L) and high (>4 mg/L) DO concentrations to understand how DO growth conditions impacted microbial community structure. Short-term batch experiments using the biomass from the parent reactors were performed under low and high DO conditions to understand how DO concentration impacts microbial physiology. Although the low DO parent biomass had a lower specific activity with respect to ammonia oxidation than the high DO parent reactor biomass, it had faster biotransformation rates of ibuprofen, sulfamethoxazole, 17α-ethinylestradiol, acetaminophen, and atenolol in high DO batch conditions. This was likely because the low DO reactor had a 2x higher biomass concentration, was enriched for ammonia oxidizers (4x higher concentration), and harbored a more diverse microbial community (3x more unique taxa) as compared to the high DO parent reactor. Overall, the results show that there can be indirect benefits from low DO operation over high DO operation that support pharmaceutical biotransformation during wastewater treatment.

Performance evaluation and microbial community of a sequencing batch biofilm reactor (SBBR) treating mariculture wastewater at different chlortetracycline concentrations

The effects of chlortetracycline (CTC) on the performance, microbial activity, extracellular polymeric substances (EPS) and microbial community of a sequencing batch biofilm reactor (SBBR) were investigated in treating mariculture wastewater. Low CTC concentration (less than 6 mg/L) had no obvious effect on the SBBR performance, whereas high CTC concentration could inhibit the chemical oxygen demand (COD) and nitrogen removal of the SBBR. The microbial activity of the biofilm in the SBBR decreased with the increase of CTC concentration from 0 to 35 mg/L. The protein (PN) contents were always higher than the PS contents in both loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) at different CTC concentrations. The chemical compositions of LB-EPS and TB-EPS had obvious variations with the increase of CTC concentration from 0 to 35 mg/L. The high-throughput sequencing revealed the effects of CTC on the microbial communities of the biofilm at phylum, class and genus level. The relative abundances of some genera displayed a decreasing tendency with the increase of CTC concentration from 0 to 35 mg/L, such as Nitrospira, Paracoccus, Hyphomicrobium, Azospirillum. However, the relative abundances of the genera Flavobacterium, Aequorivita, Buchnera, Azonexus and Thioalbus increased with the increase of CTC concentration.

New Technologies for Studying Biofilms

Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.

Tracking and quantification of nitrifying bacteria in biofilm and mixed liquor of a partial nitrification MBBR pilot plant using fluorescence in situ hybridization

A moving bead biofilm reactor (MBBR) pilot plant was implemented as a partial nitrification process for pre-treatment of ammonium-rich liquors (676 ± 195 mg L(-1)), and studied for 479 days under variations in hydraulic retention time. The main purpose of this work, was the study of dynamics abundance of total bacteria and single-cells nitrifying bacteria belonging to ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in biofilms and mixed liquor of the plant. The microbial monitoring was successfully achieved using fluorescence in situ hybridization combined with flocs disaggregation protocol as a useful microbial monitoring tool. A partial nitrification process with a N-NH4(+) removal rate of about 38.6 ± 14.8% was successfully achieved at 211 days after start-up, with a clear dominance of AOB, which accounted for 11.3 ± 17.0% of total bacterial cells compared with only 2.1 ± 4.0% of NOB. The effluent obtained was subsequently supplied to an Anammox reactor for complete ammonium treatment.

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster

BACKGROUND

Ascidians can associate with abundant and diverse consortia of microbial symbionts, yet these communities remain unexamined for the majority of host ascidians and little is known about host-symbiont interactions.

METHODS

We coupled electron microscopy and 16S rRNA gene tag pyrosequencing to investigate the bacterial communities associated with the colonial ascidian Pseudodistoma crucigaster, a species endemic to the Mediterranean Sea that has a life cycle with two phases: actively-filtering (active) and non-filtering (resting) forms.

RESULTS

Resting colonies exhibited a reduced branchial sac (feeding apparatus) and a thickened cuticle. Electron microscope images also suggested higher abundance of colonizing microorganisms on surfaces of resting colonies. Accordingly, bacterial sequences associated with environmental sources (sediment and biofilms, >99 % similarity) were detected exclusively in resting colonies. Bacterial communities of P. crucigaster colonies (active and resting) were dominated by 3 core taxa affiliated (>94 % similarity) with previously described symbiotic Alphaproteobacteria in marine invertebrates. Shifts in rare bacteria were detected when ascidians entered the resting phase, including the appearance of strictly anaerobic lineages and nitrifying bacterial guilds.

CONCLUSIONS

These findings suggest that physical (thickened cuticle) and metabolic (feeding cessation) changes in host ascidians have cascading effects on associated bacteria, where modified oxygen concentrations and chemical substrates for microbial metabolism may create anaerobic microhabitats and promote colonization by environmental microorganisms.

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

Complete nitrification by Nitrospira bacteria

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

Detection of nitrifiers and evaluation of partial nitrification for wastewater treatment: A review

Partial nitrification has gained broad interests in the biological nitrogen removal (BNR) from wastewater, since it alleviates carbon limitation issues and acts as a shortcut nitrogen removal system combined with anaerobic ammonium oxidation (Anammox) process. The occurrence and maintenance of partial nitrification relies on various conditions, which favor ammonium oxidizing bacteria (AOB) but inhibit or limit nitrite oxidizing bacteria (NOB). The studies of the AOB and NOB activities have been conducted by state-of-the-art molecular techniques, such as Polymerase Chain Reaction (PCR), Quantitative PCR, denaturing gradient gel electrophoresis (DGGE), Fluorescence in situ hybridization (FISH) technique, Terminal Restriction Fragment Length Polymorphism (T-RFLP), Live/Dead BacLight, and quinone profile. Furthermore, control strategies for obtaining partial nitrification are mainly focused on the pH, temperature, dissolved oxygen concentration, real-time aeration control, sludge retention time, substrate concentration, alternating anoxic and aerobic operation, inhibitor and ultrasonic treatment. Existing problems and further perspectives for the scale-up of partial nitrification are also proposed and suggested.

Mass spectrometric metabolomic imaging of biofilms on corroding steel surfaces using laser ablation and solvent capture by aspiration

Ambient laser ablation and solvent capture by aspiration (LASCA) mass spectrometric imaging was combined with metabolomics high-performance liquid chromatography (HPLC) mass spectrometry analysis and light profilometry to investigate the correlation between chemical composition of marine bacterial biofilms on surfaces of 1018 carbon steel and corrosion damage of steel underneath the biofilms. Pure cultures of Marinobacter sp. or a wild population of bacteria present in coastal seawater served as sources of biofilms. Profilometry data of biofilm-free surfaces demonstrated heterogeneous distributions of corrosion damage. LASCA data were correlated with areas on the coupons varying in the level of corrosion attack, to reveal differences in chemical composition within biofilm regions associated with corroding and corrosion-free zones. Putative identification of selected compounds was carried out based on HPLC results and subsequent database searches. This is the first report of successful ambient chemical and metabolomic imaging of marine biofilms on corroding metallic materials. The metabolic analysis of such biofilms is challenging due to the presence in the biofilm of large amounts of corrosion products. However, by using the LASCA imaging interface, images of more than 1000 ions (potential metabolites) are generated, revealing striking heterogeneities within the biofilm. In the two model systems studied here, it is found that some of the patterns observed in selected ion images closely correlate with the occurrence and extent of corrosion in the carbon steel substrate as revealed by profilometry, while others do not. This approach toward the study of microbially influenced corrosion (MIC) holds great promise for approaching a fundamental understanding of the mechanisms involved in MIC.