Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties

Chemomixoautotrophy and stress adaptation of anammox bacteria: A review

Anaerobic ammonium oxidizing (anammox) bacteria, which were first discovered nearly three decades ago, are crucial for treating ammonium-containing wastewater. Studies have reported on the biochemical nitrogen conversion process and the physiological, phylogenic, and ecological features of anammox bacteria. For a long time, anammox bacteria were assumed to have a lithoautotrophic lifestyle. However, recent studies have suggested the functional versatility of anammox bacteria. Genome-based analysis and experiments with enrichment cultures have demonstrated the association of the metabolic activities of anammox bacteria with different stress conditions, revealing the importance of utilizing specific organic substances, including organoautotrophy, for growth and adaptation to stress conditions. Our understanding regarding the utilization and metabolism of organic substances and their associations with anammox reactions in anammox bacteria is growing but still incomplete. In this review, we summarize the effect of the utilization of organic substances by anammox bacteria under environmental stress conditions, emphasizing their potential organoautotrophic activity and metabolic flexibility. Although most anammox bacteria may utilize specific organic substances, Ca. Brocadia exhibited the highest level of mixoautotrophic activity. The environmental factors that substantially affect the organoautotrophic activities of anammox bacteria were also examined. This review provides a new perspective on the organoautotrophic capacity of anammox bacteria.

Potential Role of the Anammoxosome in the Adaptation of Anammox Bacteria to Salinity Stress

The underlying adaptative mechanisms of anammox bacteria to salt stress are still unclear. The potential role of the anammoxosome in modulating material and energy metabolism in response to salinity stress was investigated in this study. The results showed that anammox bacteria increased membrane fluidity and decreased mechanical properties by shortening the ladderane fatty acid chain length of anammoxosome in response to salinity shock, which led to the breakdown of the proton motive force driving ATP synthesis and retarded energy metabolism activity. Afterward, the fatty acid chain length and membrane properties were recovered to enhance the energy metabolic activity. The relative transmission electron microscopy (TEM) area proportion of anammoxosome decreased from 55.9 to 38.9% under salinity stress. The 3D imaging of the anammox bacteria based on Synchrotron soft X-ray tomography showed that the reduction in the relative volume proportion of the anammoxosome and the concave surfaces was induced by salinity stress, which led to the lower energy expenditure of the material transportation and provided more binding sites for enzymes. Therefore, anammox bacteria can modulate nitrogen and energy metabolism by changing the membrane properties and morphology of the anammoxosome in response to salinity stress. This study broadens the response mechanism of anammox bacteria to salinity stress.

Deciphering performance and microbial characterization of marine anammox bacteria-based consortia treating nitrogen-laden hypersaline wastewater: Inhibiting threshold of salinity

Hypersaline wastewater posed a challenge to microbial nitrogen removal processes. Herein, halophilic marine anammox bacteria (MAB) were applied to treat nitrogen-rich wastewater with 35-90 g/L salts for the first time. It was found that MAB, with low relative abundance (2.3-6.9 %), still exhibited good nitrogen removal efficiency (>90 %) under 35-70 g/L salts. The specific anammox activity peaked at 180.16 mg N/(g·VSS·d) at 65 g/L salts. MAB secreted more extracellular polymeric substances to resist the adverse effects of hypersaline stress. Nevertheless, the nitrogen removal deteriorated at 75 g/L salts, and further collapsed as the salinity increased. At 90 g/L salts, total nitrogen removal rate decreased by 74 % compared with that of 35 g/L salts. Besides, SBR1031 increased from 12.0 % (35 g/L salts) to 17.4 % (90 g/L salts) and became the dominant bacterial genus in the reactor. This work shed light on the treatment of hypersaline wastewater through MAB.

Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago

Fossilized lipids offer a rare glimpse into ancient ecosystems. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of cyanobacteria as primary producers throughout geological history. However, the discovery of hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including recently proposed candidate phyla and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free samples. We show that HpnP was probably present in the last common ancestor of cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago (Ma). A subsequent rise of sedimentary 2-methylhopanes around 600 Ma probably reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae-possibly connected by algal dependency on microbially produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers before 750 Ma and thus as a potential tool to measure the importance of oxygenic cyanobacteria as primary producers on early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Decryption for nitrogen removal in Anammox-based coupled systems: Nitrite-induced mechanisms

This study investigated the effects of NO₂^- on synergetic interactions between Anammox bacteria (AnAOB) and sulfur-oxidizing bacteria (SOB) in an autotrophic denitrification-Anammox system. The presence of NO₂^- (0-75 mg-N/L) was shown to significantly enhance NH₄⁺ and NO₃^- conversion rates, achieving intensified synergy between AnAOB and SOB. However, once NO₂^- exceed a threshold concentration (100 mg-N/L), both NH₄⁺ and NO₃^- conversion rates decreased with increased NO₂^- consumption via autotrophic denitrification. The cooperation between AnAOB and SOB was decoupled due to the NO₂^- inhibition. Improved system reliability and nitrogen removal performance was achieved in a long-term reactor operation with NO₂^- in the influent; reverse transcription-quantitative polymerase chain reaction analysis showed elevated hydrazine synthase gene transcription levels (5.00-fold), comparing to these in the reactor without NO₂^-. This study elucidated the mechanism of NO₂^- induced synergetic interactions between AnAOB and SOB, providing theoretical guidance for engineering applications of Anammox-based coupled systems.

Insights into nitrogen removal and microbial response of marine anammox bacteria-based consortia treating saline wastewater: From high to moderate and low salinities

Marine anammox bacteria (MAB) have promising nitrogen removal performance in high saline wastewater treatment. Nevertheless, the impact resulting from moderate and low salinities on MAB is still unclear. Herein, MAB were applied to treat saline wastewater from high to moderate and low salinities for the first time. Independent of salinities (35-3.5 g/L), MAB consistently exhibited good nitrogen removal performance, and maximum total nitrogen removal rate (0.97 kg/(m³·d)) occurred at 10.5 g/L salts. More extracellular polymeric substances (EPSs) were secreted by MAB-based consortia to resist hypotonic surroundings. However, a sharp EPS decrease was accompanied by the collapse of MAB-driven anammox process, and MAB granules disintegrated due to long-term exposure to salt-free environment. The relative abundance of MAB varied from 10.7% to 15.9% and 3.8% as salinity decreased from 35 to 10.5 and 0 g/L salts. These findings will provide practical implementation of MAB-driven anammox process treating wastewater with different salinities.

Sustainable nitrogen removal in anammox-mediated systems: Microbial metabolic pathways, operational conditions and mathematical modelling

Anammox-mediated systems have attracted considerable attention as alternative cost-effective technologies for sustainable nitrogen (N) removal from wastewater. This review comprehensively highlights the importance of understanding microbial metabolism in anammox-mediated systems under crucial operation parameters, indicating the potentially wide applications for the sustainable treatment of N-containing wastewater. The partial nitrification-anammox (PN-A), simultaneous PN-A and denitrification (SNAD) processes have demonstrated sustainable N removal from sidestream wastewater. The partial denitrification-anammox (PD-A) and denitrifying anaerobic methane oxidation-anammox (DAMO-A) processes have advanced sustainable N removal efficiency in mainstream wastewater treatment. Moreover, N2O production/emission hotspots are extensively discussed in anammox-based processes and are related to the dominant ammonia-oxidizing bacteria (AOB) and denitrifying heterotrophs. In contrast, N2O is not produced in the metabolism pathways of AnAOB and DAMO-archaea; Moreover, the actual contribution of N2O production by dissimilatory nitrate reduction to ammonium (DNRA) and DAMO-bacteria in their species remains uncertain. Thus, PD-A and DAMO-A processes would achieve reduction in greenhouse gas production, as well as energy consumption for the reliability of N removal efficiencies. In addition to reaction mechanisms, this review covers the mathematical models for simultaneous anammox, partial nitrification and/or denitrification (i.e., PN-A, PD-A, and SNAD). Promising NO3- reduction technologies by endogenous PD, sulfur-driven autotrophic denitrification, and DNRA by anammox are also discussed. In summary, this review provides a better understanding of sustainable N removal in anammox-mediated systems, thereby encouraging future investigation and exploration of the sustainable N bio-treatment from wastewater.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

Long-term adaptation of two anammox granules with different ratios of Candidatus Brocadia and Candidatus Jettenia under increasing salinity and their application to treat saline wastewater

Nitrogen removal in saline wastewater is a challenge of the anaerobic ammonium oxidation (anammox) process, which is dominated by freshwater anammox bacteria (FAB). Candidatus Brocadia and Candidatus Jettenia, the most widely used FABs, have been separately applied and evaluated for their ability to treat saline wastewater. To understand the effect of salinity on nitrogen removal capability when they present together in an anammox granule, we compared two anammox granules: GRN1 was evenly dominated by Ca. Brocadia (42 %) and Ca. Jettenia (43 %), while GRN2 was dominated with mostly Ca. Brocadia (90 %) and a small amount of Ca. Jettenia (1 %). Each granule was inoculated into a continuous column reactor to treat artificial wastewater containing 150 mg NH₄⁺-N/L and 150 mg NO₂^--N/L under increasing saline conditions for 250 days. GRN1 showed superior and more stable nitrogen removal than GRN2 under saline conditions of up to 15 g NaCl/L. Under high-saline conditions, both the granules' sizes decreased (larger GRN1 than GRN2 in initial). The mass percent of Na salt increased (more in GRN2) and mineral contents decreased more in GRN1. High-throughput sequencing for microbial community analysis showed that Planctomycetes in GRN1 (85 %) and GRN2 (92 %) decreased to 14 % and 12 %, respectively. The ratio of Ca. Brocadia and Ca. Jettenia in GRN1 changed to 37 % and 63 %, respectively, whereas the ratio in GRN2 (99 % and 1 %, respectively) did not change. Both salt-adapted granules were applied to the two-stage partial nitritation and anammox (PN/A) process to treat high strength ammonium (400 mg/L) wastewater under high saline condition (15 g NaCl/L). The PN/A process containing GRN1 showed more stable nitrogen removal performance during approximately 100 days of operation. These results suggest that the anammox granules evenly dominated by two FABs, Ca. Brocadia and Ca. Jettenia, would be advantageous to treat high-strength NH₄⁺ wastewater under high-saline conditions.

Effects of silver nanoparticles on denitrification and anammox in sediments of hypertrophic and mesotrophic lakes

The abundant production and wide usage of silver nanoparticles (Ag NPs) inevitably lead to their release into aquatic ecosystems. However, it is still unclear about how Ag NPs influence denitrification and anammox (DA) in freshwater sediments. To address this, the sediments of hypertrophic and mesotrophic lakes were exposed to 0.5 and 50 mg/L Ag NPs under anaerobic conditions for 7 days to explore the effects of Ag NPs on environmental variables, including redox potential (Eh), pH, organic matter (OM) and acid volatile sulfide (AVS), and the resulting influence on DA. Experimental results indicated that NO₃^--N and NH₄⁺-N levels were increased by the low (p > 0.05) and high doses of Ag NPs (p < 0.05) in comparison with the non-Ag control, revealing an inhibitive impact on DA. The level of total nitrogen (TN) was notably increased by the low and high doses of Ag NPs (p < 0.05), perhaps due to inhibited enzyme activity and corresponding encoding gene abundance, which were related to generating gaseous nitrogen such as N₂O and N₂. In addition, environmental factor Eh was significantly raised by Ag NPs (p < 0.05), further inhibiting DA. Moreover, the quantitative analysis unveiled that denitrifying and anammox bacteria in hypertrophic lakes evinced a stronger resistance to Ag NPs toxicity than those in mesotrophic lakes. Overall, our study revealed that short-term exposure to Ag NPs could inhibit DA in sediments. These findings provide an understanding enabling evaluation and prediction of the environmental risks of Ag NPs in freshwater lakes.

Microbial diversity across compartments in an aquaponic system and its connection to the nitrogen cycle

Aquaponics combines hydroponic crop production with recirculating aquaculture. These systems comprise various compartments (fish tank, biofilter, sump, hydroponic table, radial flow settler and anaerobic digester), each with their own specific environmental pressures, which trigger the formation of unique microbial communities. Triplicated aquaponic systems were used to investigate the microbial community composition during three lettuce growing cycles. The sampling of individual compartments allowed community patterns to be generated using amplicon sequencing of bacterial and archaeal 16S rRNA genes. Nitrifying bacteria were identified in the hydroponic compartments, indicating that these compartments may play a larger role than previously thought in the system's nitrogen cycle. In addition to the observed temporal changes in community compositions within the anaerobic compartment, more archaeal reads were obtained from sludge samples than from the aerobic part of the system. Lower bacterial diversity was observed in fresh fish feces, where a highly discrete gut flora composition was seen. Finally, the most pronounced differences in microbial community compositions were observed between the aerobic and anaerobic loops of the system, with unique bacterial compositions in each individual compartment.

Distinctive differences in the granulation of saline and non-saline enriched anaerobic ammonia oxidizing (AMX) bacteria

The growing interest in the anaerobic ammonium oxidizing (AMX) process in treating high nitrogen containing wastewaters and a comprehensive study into the granulation mechanism of these bacteria under diverse environmental conditions over the years have been unequal. To this effect, the distinctive differences in saline adapted AMX (S_AMX) and non-saline adapted AMX (NS_AMX) granules are presented in this study. It was observed that substrate utilisation profiles, granule formation mechanism, and pace towards granulation differed marginally for the two adaptation conditions. The different microbial dominant aggregation types aided in splitting the 471 days operated lab-scale SBRs into three distinct phases. In both reactors, phase III (granules dominant phase) showed the highest average nitrogen removal efficiency of 87.9% ± 4.8% and 85.6% ± 3.6% for the S_AMX and NS_AMX processes, respectively. The extracellular polymeric substances (EPS) quantity and major composition determined its role either as a binding agent in granulation or a survival mechanism in saline adaptation. It was also observed that granules of the S_AMX reactor were mostly loosely and less condensed aggregates of smaller sub-units and flocs while those of the NS_AMX reactor were compact agglomerates. The ionic gradient in saline enrichment led to an increased activity of the Na⁺/K⁺ - ATPase, hence enriched granules produced higher cellular adenosine triphosphate molecules which finally improved the granules active biomass ratio by 32.96%. Microbial community showed that about three to four major known AMX species made up the granules consortia in both reactors. Proteins and expression of functional genes differed for these different species.

Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges

The various forms of nitrogen (N), including ammonium (NH₄⁺), nitrite (NO₂^-), and nitrate (NO₃^-), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox) and partial denitrification and anammox (PD/anammox) have been universally acknowledged to consider as alternatives, promising and cost-effective technologies for sustainable N removal from wastewaters compared to nitrification-denitrification processes. This review comprehensively presents and discusses the latest advances in BNR technologies, including traditional nitrification-denitrification and anammox-based systems. To a deep understanding of a better-controlled combining anammox with traditional processes, the microbial community diversity and metabolism, as well as, biomass morphological characteristics were clearly reviewed in the anammox-based systems. Explaining simultaneous microbial competition and control of crucial operation parameters in single-stage anammox-based processes in terms of optimization and economic benefits makes this contribution a different vision from available review papers. The most important sustainability indicators, including global warming potential (GWP), carbon footprint (CF) and energy behaviours were explored to evaluate the sustainability of BNR processes in wastewater treatment. Additionally, the challenges and solutions for BNR processes are extensively discussed. In summary, this review helps facilitate a critical understanding of N removal technologies. It is confirmed that sustainability and saving energy would be achieved by anammox-based systems, thereby could be encouraged future outcomes for a sustainable N removal economy.

Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments

The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.

Nitrogen removal characteristics of biofilms in each area of a full-scale AAO oxidation ditch process

Plastic carriers were installed in different areas of a full-scale anaerobic/anoxic/aerobic (AAO) oxidation ditch process, and the dynamics of nitrogen removal, biofilm morphologies, and microorganism species were investigated. The results showed that the biofilm at the front of the aerobic area (dissolved oxygen [DO] = 0.93 mg L^-1) provided the best denitrification, with specific nitrate and nitrite reduction rates of 10.16 and 3.78 mg·(g·h)^-1, respectively. The biofilm in the middle of the aerobic area (DO = 1.27 mg L^-1) exhibited the best nitrification performance, with a maximum specific ammonia oxidation rate of 3.21 mg·(g·h)^-1. The biofilm at the end of the aerobic area (DO = 0.01 mg L^-1) exhibited the highest anammox potential with a maximum specific anammox rate of 0.67 mg·(g·h)^-1. No correlation was observed between the specific nitrogen removal rates and abundance of nitrogen-removing microorganisms at the genus level. Biofilm denitrification during the process was primarily completed by heterotrophic denitrifying bacteria (Thauera, Acinetobacter, Hyphomicrobium, and Thermomonas). Aerobic denitrifying bacteria (0.19% Thauera and 0.34% Hyphomicrobium) were identified as the main denitrifying bacteria in the middle of the aerobic area. The dominant nitrifying microorganisms in the middle of the aerobic area were Nitrosomonas (0.50%) and Nitrospira (1.04%). A biofilm in the end of the aerobic area exhibited specific anammox potential, which may have been related to the dominance of 0.024% Candidatus Brocadia. Kinetic analysis revealed that adding plastic carriers to the front and middle of the aerobic area contributed to stable nitrogen removal efficiency.

Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes

The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation. Routine process parameters were surveyed and the response and evolution of the microbiota was followed by molecular tools, ex-situ activity tests and further, AnAOB quantification through particle tracking and heme measurement. After eight months of operation, the first anaerobic, simultaneous depletion of ammonia and nitrite was observed ex-situ, together with a direction to higher nitrite generation (68% of total NO_x-N) as compared to nitrate under aerobic conditions. Our dissolved oxygen (DO) scheme allowed for transient anoxic conditions and had a strong influence on nitrite levels and the NOB community, where Nitrobacter eventually dominated Nitrospira. The establishment of a minor but stable AnAOB biomass was accompanied by the rise of Chloroflexi and distinct emergence of Chlorobi, a trend not seen in the sidestream system. Interestingly, the most pronounced switch in the microbial community and noticeable NOB repression occurred during unfavorable conditions, i.e. the cold winter season and high organic load. Further abatement of NOB was achieved through bioaugmentation of aerobic ammonia oxidizing bacteria (AerAOB) from the sidestream-DEMON® tank. Performance of the sidestream pN/A was not impaired by this operational scheme and the average volumetric nitrogen removal rate of the mainstream even doubled in the second half of the monitoring campaign. We conclude that a combination of both, regular sidestream-DEMON® biomass transfer and granular SRT increase via hydrocyclone operation was crucial for AnAOB establishment within the mainstream.

Technologies for Biological and Bioelectrochemical Removal of Inorganic Nitrogen from Wastewater: A Review

Water contamination due to various nitrogenous pollutants generated from wastewater treatment plants is a crucial and ubiquitous environmental problem now-a-days. Nitrogen contaminated water has manifold detrimental effects on human health as well as aquatic life. Consequently, various biological treatment processes are employed to transform the undesirable forms of nitrogen in wastewater to safer ones for subsequent discharge. In this review, an overview of various conventional biological treatment processes (viz. nitrification, denitrification, and anammox) have been presented along with recent novel bioelectrochemical methods (viz. microbial fuel cells and microbial electrolysis cells). Additionally, nitrogen is an indispensable nutrient necessary to produce artificial fertilizers by fixing dinitrogen gas from the atmosphere. Thus, this study also explored the potential capability of various nitrogen recovery processes from wastewater (like microalgae, cyanobacteria, struvite precipitation, stripping, and zeolites) that are used in industries. Further, the trade-offs, challenges posed by these processes have been dwelt on along with other biological processes like CANON, SHARON, OLAND, and others.

Microbiomes and Planctomycete diversity in large-scale aquaria habitats

In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1–15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.

Modeling of sulfur-driven autotrophic denitrification coupled with Anammox process

While sulfur-driven autotrophic denitrification (SDAD) occurring in the anoxic reactor of the sulfate reduction, autotrophic denitrification and nitrification integrated (SANI) system has been regarded as the main nitrogen removal bioprocess, little is known about the accompanying Anammox bacteria whose presence is made possible by the co-existence of NH₄⁺ and NO₂^-. Therefore, this work firstly developed an integrated SDAD-Anammox model to describe the interactions between sulfur-oxidizing bacteria and Anammox bacteria. The model was subsequently used to explore the impacts of influent conditions on the reactor performance and microbial community structure of the anoxic reactor. The results revealed that at a relatively low ratio of <1.5 mg S/mg N, Anammox bacteria could survive and even take a dominant position (up to 58.9%). Finally, a modified SANI system configuration based on the effective collaboration between SDAD and Anammox processes was proposed to improve the efficiency of the treatment of sulfate-rich saline sewage.

A comprehensive root cause analysis of anammox bioreactor performance decline

The cultivation of anaerobic ammonia oxidizing bacteria (anammox) has gained enormous awareness over the last few decades. Although numerous studies focus massively on successfully growing these anammox to different enrichment environments, in reality, the failure rates are somewhat comparable to the reported success rates. This study combines a variety of measurement techniques to observe and monitor the sequence of a bioreactor performance decline following elevated influent substrate concentration. After attaining stable substrate removal throughout a nitrogen loading rate (NLR) range of 0.691 to 1.669 kg-N·m^-3·d^-1, the performance of the lab-scale anammox-sequencing batch reactor (SBR) abruptly broke down as the NLR reached 2.01 kg-N·m^-3·d^-1. The gathered information showed that the increased NLR firstly caused a significant and unfavorable change in the free ammonia (FA) and free nitrous acid (FNA) concentration in the bioreactor. A subsequent drop in N₂ production and a decline from a peak high of 0.381 to a low of 0.012 kg-N·kg-VSS^-3·d^-1 of the specific nitrogen removal rate (SNRR) led to an 82% absurd decline in microbial cellular energy production. Prior to these anammox switching to survival mode and secreting larger quantities (32% higher) of extracellular polymeric substances (EPS), the activity of syntrophic decomposers increased substantially leading to the internal production of excess CO₂ in the bioreactor and thereby diverging the bioreactor pH to lower levels. The purposes of this study are to understand the reason an anammox process shows different signals during a decline phase and to enable immediate response to performance deterioration.

Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes

Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.

Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers

Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon-poor environments. However, the diversity and prevalence of anammox bacteria in the terrestrial subsurface-a typically oligotrophic environment-are little understood. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analyzed 16S rRNA genes and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells and metagenomes and metatranscriptomes from an oxic-to-dysoxic subset. Data indicate that anammox and anammox-associated bacteria (class "Candidatus Brocadiae") are prevalent in the aquifers studied, and that anammox community composition is strongly differentiated by dissolved oxygen (DO), but not ammonia/nitrite. While "Candidatus Brocadiae" diversity decreased with increasing DO, "Candidatus Brocadiae" 16S rRNA genes and hydrazine synthase (hzsB) genes and transcripts were detected across a wide range of bulk groundwater DO concentrations (0 to 10 mg/L). Anammox genes and transcripts correlated significantly with those involved in aerobic ammonia oxidation (amoA), potentially representing a major source of nitrite for anammox. Eight "Candidatus Brocadiae" genomes (63 to 95% complete), representing 2 uncharacterized families and 6 novel species, were reconstructed. Six genomes have genes characteristic of anammox, all for chemolithoautotrophy. Anammox and aerotolerance genes of up to four "Candidatus Brocadiae" genomes were transcriptionally active under oxic and dysoxic conditions, although activity was highest in dysoxic groundwater. The coexpression of nrfAH nitrite reductase genes by "Candidatus Brocadiae" suggests active regeneration of ammonia for anammox. Our findings indicate that anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, which is likely supported by nitrite from aerobic ammonia oxidation. IMPORTANCE Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant. Our research confirms that anammox bacteria and the anammox process are prevalent in aquifers and occur across diverse lithologies (e.g., sandy gravel, sand-silt, and volcanic) and groundwater physicochemistries (e.g., various oxygen, carbon, nitrate, and ammonium concentrations). Results reveal niche differentiation among anammox bacteria largely driven by groundwater oxygen contents and provide evidence that anammox is supported by proximity to oxic niches and handoffs from aerobic ammonia oxidizers. We further show that this process, while anaerobic, is active in groundwater characterized as oxic, likely due to the availability of anoxic niches.

Microalgae-based swine wastewater treatment: Strain screening, conditions optimization, physiological activity and biomass potential

Using microalgae to treat swine wastewater (SW) can achieve wastewater purification and biomass recovery at the same time. The algae species suitable for growth in SW were screened in this study, and the response surface combined with the desirability function method was used for multi-objective optimization to obtain high algal biomass and pollutant removal. Chlorophyll fluorescence parameters and biomass composition were analyzed to evaluate the cell physiological activity and its application potential. Chlorella sp. HL was selected as the most suitable species for growth in SW, and after 9 d of cultivation, the maximum specific growth rate and highest algal density were achieved 0.51 d^-1 and 2.43 × 10⁷ cells/mL, respectively. In addition, the removal of total phosphate and chemical oxygen demand were reached 69.13% and 72.95%, respectively. The optimum conditions for maximum algal density and highest pollutant removal were determined as the light intensity of 58.73 μmol/m²/s, inoculation density of 5.0 × 10⁶ cells/mL, and a light/dark ratio of 3 using response surface model, and the predicted overall desirability value was 0.96. The potential maximum quantum yield of PSII (Fv/Fm) of Chlorella sp. HL in the early stage of cultivation was 0.60-0.70, while under high light and long photoperiod, the value of Fv/Fm and performance index of Chlorella decreased, trapped and dissipated energy flux per reaction center increased. The higher heating value of 18.25 MJ/kg indicated that the Chlorella cultivated in SW could be a good feedstock for biofuel production.

A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium

The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.

Assessment of Ammonia as a Biosignature Gas in Exoplanet Atmospheres

Ammonia (NH₃) in a terrestrial planet atmosphere is generally a good biosignature gas, primarily because terrestrial planets have no significant known abiotic NH₃ source. The conditions required for NH₃ to accumulate in the atmosphere are, however, stringent. NH₃'s high water solubility and high biousability likely prevent NH₃ from accumulating in the atmosphere to detectable levels unless life is a net source of NH₃ and produces enough NH₃ to saturate the surface sinks. Only then can NH₃ accumulate in the atmosphere with a reasonable surface production flux. For the highly favorable planetary scenario of terrestrial planets with hydrogen (H₂)-dominated atmospheres orbiting M dwarf stars (M5V), we find that a minimum of about 5 ppm column-averaged mixing ratio is needed for NH₃ to be detectable with JWST, considering a 10 ppm JWST systematic noise floor. When the surface is saturated with NH₃ (i.e., there are no NH₃-removal reactions on the surface), the required biological surface flux to reach 5 ppm is on the order of 10¹⁰ molecules/(cm²·s), comparable with the terrestrial biological production of methane (CH₄). However, when the surface is unsaturated with NH₃, due to additional sinks present on the surface, life would have to produce NH₃ at surface flux levels on the order of 10¹⁵ molecules/(cm²·s) (∼4.5 × 10⁶ Tg/year). This value is roughly 20,000 times greater than the biological production of NH₃ on the Earth and about 10,000 times greater than Earth's CH₄ biological production. Volatile amines have similar solubilities and reactivities to NH₃ and hence share NH₃'s weaknesses and strengths as a biosignature. Finally, to establish NH₃ as a biosignature gas, we must rule out mini-Neptunes with deep atmospheres, where temperatures and pressures are high enough for NH₃'s atmospheric production.

Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers

Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.

The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes

The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.

Variations of N concentrations and microbial community in the start-up of anammox using anaerobic heterotrophic sludge: Influence of a long reaction-phase time and comparison of the efficiencies of attached-versus suspended-growth cultures

Anaerobic sludge was capable of producing anaerobic ammonium oxidation (anammox) cultures. However, the low activity of anammox bacteria in the seed sludge often led to a long time for stable anammox to initiate. The objective of this study was to investigate the influence of an extended reaction-phase time in the sequencing batch reactor (SBR) on the rapid startup of anaerobic ammonium oxidation (anammox) using anaerobic heterotrophic bacteria as the seed sludge. After the startup, suspended and attached bacteria in anammox were separately analyzed for comparison. The variations of nitrogen concentrations and shifts of the microbial community structures were studied. The results showed that anammox occurred after a long reaction-phase time in the SBR with the efficient removals of NH₄⁺ (96.4%) and NO₂^- (99.8%). The effective NO₂^- treatment before anammox startup was attributable to inevitable denitrification or dissimilatory nitrate reduction (e.g., Denitratisoma). The occurrence of anammox was supported by the anammox stoichiometry, bacteria diversity variation, and principal component analysis. The overall nitrogen removal rate (NRR) and nitrogen removal efficiency (NRE) was 0.07 kg/m³-d and 92.8%, respectively. The relative molar quantities of NH₄⁺ and NO₂^- removed as well as N₂ and NO₃^- formed were 1(1):1.29(1.32):1.45(1.02):0.15(0.26), as the numbers in the parentheses represent the theoretical values. Denitratisoma and Desulfatiglans dominated in the seed sludge, whereas Candidatus_Jettenia abundances were significantly higher in anammox attached- (26.0%) and suspended-growth cultures (14.5%). Fifty-three genera were simultaneously identified in all samples, suggesting their importance in the startup of anammox from anaerobic sludge. Candidatus_Jettenia was observed to be more associated with the growth of anammox biofilm (the abundances were 26.0% and 14.5% in attached- and suspended-growth cultures, respectively) and supported the fine nitrogen removal performance in the attached-growth cultures.

Novel and Conventional Isolation Techniques to Obtain Planctomycetes from Marine Environments

Bacteria from the distinctive Planctomycetes phylum are well spread around the globe; they are capable of colonizing many habitats, including marine, freshwater, terrestrial, and even extreme habitats such as hydrothermal vents and hot springs. They can also be found living in association with other organisms, such as macroalgae, plants, and invertebrates. While ubiquitous, only a small fraction of the known diversity includes axenic cultures. In this study, we aimed to apply conventional techniques to isolate, in diverse culture media, planctomycetes from two beaches of the Portuguese north-coast by using sediments, red, green, and brown macroalgae, the shell of the mussel Mytilus edulis, an anemone belonging to the species Actinia equina, and seawater as sources. With this approach, thirty-seven isolates closely related to seven species from the families Planctomycetaceae and Pirellulaceae (class Planctomycetia) were brought into pure culture. Moreover, we applied an iChip inspired in-situ culturing technique to successfully retrieve planctomycetes from marine sediments, which resulted in the isolation of three additional strains, two affiliated to the species Novipirellula caenicola and one to a putative novel Rubinisphaera. This work enlarges the number of isolated planctomycetal strains and shows the adequacy of a novel methodology for planctomycetes isolation.

Dynamics of Microbial Community During Nitrification Biofilter Acclimation with Low and High Ammonia

The acclimation of a nitrifying biofilter is a crucial and time-consuming task for setting up a recirculating aquaculture system (RAS). Gaining a better understanding of the dynamics of the microbial community during the acclimation period in the system could be useful for the development of mature nitrifying biofilters. In this study, high-throughput DNA sequencing was applied to monitor the microbial communities on a biofilter during the acclimation period (7 weeks) in high (100 mg N/L) and low (5 mg N/L) total ammonia nitrogen (TAN) treatments. Both treatments were successful for developing a mature nitrifying biofilter, dominated by Proteobacteria, Bacteroidetes, and Nitrospirae. Complete nitrification was found after 7 days of biofilter acclimation as indicated by decreasing TAN concentration, increasing nitrate concentration, and high abundances of the nitrifying bacteria, Nitrosomonadaceae and Nitrospiraceae. The beta diversity analysis of microbial communities showed different clustering of the samples between high and low TAN treatment groups. A greater abundance of nitrifying bacteria was found in the high TAN treatments (27-51%) than in the low TAN treatment (15-29%). The bacterial diversity in biofilters acclimated at high TAN concentration (Shannon's index 5.40-6.15) were lower than those found at low TAN treatment levels (Shannon's index 6.40-7.01). The higher diversity in biofilters acclimated at low TAN concentrations, consisting of Planctomycetes and Archaea, might benefit the nutrient recycling in the system. Although nitrification activity was observed from the first week of the acclimation period, the acclimation period should be taken as at least 6 weeks for full development of nitrifying biofilm. Moreover, the reduction of potentially pathogenic Vibrio on biofilters was found at that period.

The physiological potential of anammox bacteria as revealed by their core genome structure

We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2− reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH₂OH by self-production for anammox metabolism.

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.

Up to 40% of the ocean’s fixed nitrogen is lost in oxygen minimum zones (OMZs) by anammox, but despite the importance of this process, nitrogen loss patterns in OMZs are difficult to predict. Here the authors show that ammonium release from small particles is a major control of anammox in the Peruvian OMZ.

Long-term redox conditions in a landfill-leachate-contaminated groundwater

Indicators of redox conditions; oxygen, sulphate, nitrate, ammonium, iron and manganese, and in addition, bicarbonate and total organic carbon were studied in groundwater samples contaminated by leachate emanating from Revdalen Landfill (Norway). Based on these variables, the study aimed to deduce the redox conditions in the aquifer. Literature on landfill leachate contamination of confined aquifers is scarce and to the best of our knowledge, this study, which describes long-term analysis of redox chemistry, is the first of its kind in such an environment. Groundwater samples were monitored for a period of 24 years, enabling us to describe redox conditions on both short-term and long-term bases. Levels of measured parameters in the contaminated aquifer varied spatially and with time, but were generally elevated except oxygen; pH (4.9-8.8), oxygen (0-11.3 mg/L), sulphate (0-28 mg/L), nitrate (0-16 mg N/L), ammonium (0.02-40 mg/L), iron (0-99 mg/L), manganese (0.06-16 mg/L), bicarbonate (22-616 mg/L) and total organic carbon (1.3-47 mg/L). From the result, levels of iron, manganese, nitrate and ammonium violated the Norwegian drinking water norms. However, iron, ammonium, total organic carbon and bicarbonate showed strong attenuation along the groundwater flow path. By contrast, oxygen, nitrate and sulphate increased farther out in the plume. The redox conditions that developed in the aquifer were similar to those previously reported for phreatic aquifers, structuring by proximity to the landfill as sulphate-reducing, iron-reducing, manganese-reducing, nitrate-reducing, and finally aerobic condition. Eventually, there was an apparent breakdown of this system due to ecosystem shift in the landfill when leachable reduced ions were depleted and the landfill became aerobic. Overall, the redox framework provided remarkable attenuation to contaminants, and thus prevented potential degradation of ecological health due to the landfill leachate.

Natural attenuation of lead by microbial manganese oxides in a karst aquifer

Lead is a toxic environmental contaminant associated with current and historic mine sites. Here we studied the natural attenuation of Pb in a limestone cave system that receives drainage from the ancient Priddy Mineries, UK. Extensive deposits of manganese oxides were observed to be forming on the cave walls and as coatings in the stream beds. Analysis of these deposits identified them as birnessite (δ-MnO₂), with some extremely high concentrations of sorbed Pb (up to 56 wt%) also present. We hypothesised that these cave crusts were actively being formed by microbial Mn(II)-oxidation, and to investigate this the microbial communities were characterised by DNA sequencing, enrichment and isolation experiments. The birnessite deposits contained abundant and diverse prokaryotes and fungi, with ~5% of prokaryotes and ~ 10% of fungi closely related to known heterotrophic Mn(II)-oxidisers. A substantial proportion (up to 17%) of prokaryote sequences were assigned to groups known as autotrophic ammonia and nitrite oxidisers, suggesting that nitrogen cycling may play an important role in contributing energy and carbon to the cave crust microbial communities and consequently the formation of Mn(IV) oxides and Pb attenuation. Enrichment and isolation experiments showed that the birnessite deposits contained Mn(II)-oxidising microorganisms, and two isolates (Streptomyces sp. and Phyllobacterium sp.) could oxidise Mn(II) in the presence of 0.1 mM Pb. Supplying the enrichment cultures with acetate as a source of energy and carbon stimulated Mn(II)-oxidation, but excess organics in the form of glucose generated aqueous Mn(II), likely via microbial Mn(IV)-reduction. In this karst cave, microbial Mn(II)-oxidation contributes to the active sequestration and natural attenuation of Pb from contaminated waters, and therefore may be considered a natural analogue for the design of wastewater remediation systems and for understanding the geochemical controls on karst groundwater quality, a resource relied upon by billions of people across the globe.

Stepwise treatment of undiluted raw piggery wastewater, using three microalgal species adapted to high ammonia

A high ammonia concentration and chemical oxygen demand (COD) in piggery wastewater force it to be diluted before conventional microalgal treatment to reduce ammonia toxicity. Incomplete treatment of ammonia and COD in piggery wastewater may cause eutrophication, resulting in algal blooms. This study tried to treat raw piggery wastewater without dilution, using three strains of microalgae (Chlorella sorokiniana, Coelastrella sp. and Acutodesmus nygaardii) that outcompeted other algae under heterotrophic, mixotrophic, and autotrophic conditions, respectively, through adaptive evolution at high ammonia concentration. The three stepwise processes were designed to remove (1) small particles, COD, and phosphorus in the 1st heterotrophic C. sorokiniana cultivation, (2) ammonia and COD in the 2nd mixotrophic Coelastrella sp. cultivation, and (3) the remaining ammonia in the 3rd photoautotrophic A. nygaardii cultivation. To enhance ammonia uptake rate, each algal species were inoculated after 2-day nitrogen starvation. When the N-starved three species were inoculated at each step sequentially at 7 g/L for 2 days, the final phosphorus, COD, and ammonia removal efficiencies were 100% (16.4-0 mg/L), 92% (6820-545 mg/L), 90% (850-81 mg/L) and turbidity (99%) after total 6 days.

A critical review on the effects of antibiotics on anammox process in wastewater

Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

16S rRNA gene-based primer pair showed high specificity and quantification accuracy in detecting freshwater Brocadiales anammox bacteria

Anaerobic ammonium oxidizing (anammox) bacteria are widely distributed and contribute significantly to the global nitrogen cycle. Traditionally, identification and quantification based on the 16S rRNA gene were considered not reliable because of low 16S rRNA gene sequence identity within Brocadiales. Here we hypothesize that by using appropriate primers and methodology, 16S-based detection and quantification of anammox bacteria can be accurate. We modified an existing 16S rRNA gene-based primer pair (Amx694F-Amx960R) by changing one nucleotide (Amx694F position 18, G→C) (Amx694PF-Amx960R) so that they match the sequences of most Brocadiales anammox bacteria, and evaluated the modified primer pair with 29 freshwater samples from microcosms, anammox reactors and wastewater treatment plants of various geographical origins. The primer pair showed high specificity in detection and quantification of anammox populations in samples that contained >0.1% anammox bacteria. Quantification of anammox abundance by quantitative real-time PCR and delineation of anammox species by denaturing gradient gel electrophoresis agreed well with amplicon sequencing results. A clear shift of anammox population towards 'Candidatus Kuenenia' was observed under laboratory cultivation conditions. With the help of amplicon sequencing, we demonstrated that 16S rRNA gene-based anammox-specific primers are able to achieve qualitative and quantitative monitoring of anammox communities in wastewater treatment plants and natural freshwater environments.2007;73:5261-7.

Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches

Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series ¹³C and ²H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis. Our findings confirm predicted metabolic pathways used for CO₂ fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of the oxidative branch of an incomplete tricarboxylic acid cycle for alpha-ketoglutarate biosynthesis, despite the genome not having an annotated citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood–Ljungdahl pathway instead of oxidizing it completely to CO₂ followed by reassimilation. In contrast, our data suggest that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.

Characterization of membrane-bound metalloproteins in the anaerobic ammonium-oxidizing bacterium "Candidatus Kuenenia stuttgartiensis" strain CSTR1

Membrane-bound metalloproteins are the basis of biological energy conservation via respiratory processes, however, their biochemical characterization is difficult. Here, we followed a gel-based proteomics and metallomics approach to identify membrane-associated metalloproteins in the anaerobic ammonium-oxidizing "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Membrane-associated protein complexes were separated by two dimensional Blue Native/SDS gel electrophoresis and subunits were identified by mass spectrometry; protein-bound metal ions were quantified from the gel by connecting either a desolvating nebulizer system or laser ablation to inductively coupled plasma triple quadrupole mass spectrometry (ICP-QqQ-MS). We identified most protein complexes predicted to be involved in anaerobic ammonium oxidation and carbon fixation. The ICP-QqQ-MS data showed the presence of Fe and Zn in a wide range of high molecular weight protein complexes (230-800 kDa). Mo was prominently found in gel slices with proteins of a size of 500-650 kDa, whereas Ni was only found using the desolvating nebulizer system in the protein range of 350-500 kDa. The detected protein complexes and their metal content were consistent with genome annotations. Gel-based metalloproteomics is a sensitive and reliable approach for the characterization of metalloproteins and could be used to characterize many multimeric metalloprotein complexes in biological systems.

Simultaneous nitrification-denitrification by phosphate accumulating microorganisms

Nitrogen and phosphorous are important inorganic water pollutants that pose a major threat to the environment and health of both humans and animals. The physical and chemical ways to remove these pollutants from water and soil are expensive and harsh, so biological removal becomes the method of choice to alleviate the problem without any side effects. The identification of microorganisms capable of simultaneous heterotrophic nitrification and aerobic denitrification has greatly simplified the sequestration of nitrogen from ammonium (NH₄⁺) into dinitrogen (N₂). Further, the discovery of phosphorous accumulating organisms offers greater economic benefits because these organisms can favourably and simultaneously remove both nitrogen and phosphorous from wastewaters hence reducing the nutrient burden. The stability of the system and removal efficiency of inorganic pollutants can be enhanced by the use of immobilized organisms. However, limited work has been done so far in this direction and there is a need to further the efforts towards refining process efficiency by testing low-cost substrates and diverse microbial populations for the total eradication of these contaminants from wastewaters.

Process performance and anammox community diversity in a deammonification reactor under progressive nitrogen loading rates for swine wastewater treatment

The performance of a deammonification reactor fed with increasing nitrogen loading rates (NLR) was evaluated. The digestate from a continuous stirred tank reactor (CSTR) treating sludge from a swine production unit was diluted to provide different ammonia concentrations. The biomass samples from the end of each experimental phase were analyzed for microorganism community evaluation. The results proved that deammonification system supported a NLR up to 3.27 ± 0.13 g N L^-1 d^-1 with nitrogen removal efficiency of 83%. The specific ammonia consumption rate (µ_NH3-N) did not decrease up to this NLR proving the stability of reactor performance. Anammox bacteria genus shifted along the experiment and at the end the predominant anammox bacteria found in the reactor was candidatus Brocadia. Finally, it was proved that a deammonification reactor for nitrogen removal from CSTR digestate could be easily controlled only by monitoring pH and dissolved oxygen.

The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks

The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.

Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

Anaerobic ammonium-oxidizing (anammox) bacteria, members of the "Candidatus Brocadiaceae" family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-enclosed compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic-, and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbor multiple copies of ammonium-, nitrite-, and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite-, and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells showed that four of the seven ammonium transporter homologs and two of the nine nitrite transporter homologs were significantly upregulated during ammonium-limited growth, while another ammonium transporter- and four nitrite transporter homologs were upregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.

Leachate treatment and electricity generation using an algae-cathode microbial fuel cell with continuous flow through the chambers in series

Algae-cathode microbial fuel cells (MFCs) with various hydraulic retention times (HRTs) were investigated for electricity generation, and chemical oxygen demand (COD) and nutrient removal from diluted landfill leachate (15% v/v). The cell voltage and dissolved oxygen (DO) in the cathode were considerably affected by the HRT. The highest cell voltage was 303 mV at 20-h HRT, and DO concentration of 5.3 mg/L was only observed at 60-h HRT. Nutrient removal increased with increasing HRTs, and the maximum removal efficiency was 76.4% and 86.3% at 60-h HRT for ammonium and phosphorus, respectively. The highest COD removal of 26% was observed at 60-h HRT. The dominant phyla in the cathode were Proteobacteria, Cyanobacteria, Bacteroidetes, and Chlorophyta, which could have contributed to electricity generation and nutrient removal. This study suggests that an algae-cathode MFC with an appropriate HRT can continuously generate electricity and simultaneously remove nutrients from real leachate wastewater in field applications.