Taxis response of various denitrifying bacteria to nitrate and nitrite

Enhanced nitrogen removal of the anaerobic ammonia oxidation process by coupling with an efficient nitrate reducing bacterium (Bacillus velezensis M3-1)

Bacillus velezensis M3-1 strain isolated from the sediment of Myriophyllum aquatium constructed wetlands was found to efficiently convert NO3--N to NO2--N, and the requirements for carbon source addition were not very rigorous. This work demonstrates, for the first time, the feasibility of using the synergy of anammox and Bacillus velezensis M3-1 microorganisms for nitrogen removal. In this study, the possibility of M3-1 that converted NO3--N produced by anammox to NO2--N was verified in an anaerobic reactor. The NO3--N reduction ability of M3-1 and denitrifying bacteria in coupling system was investigated under different C/N conditions, and it was found that M3-1 used carbon sources preferentially over denitrifying bacteria. By adjusting the ratio of NH4+-N to NO2--N, it was found that the NO2--N converted from NO3--N by M3-1 participated in the original anammox.The nitrogen removal efficacy (NRE) of the coupled system was increased by 12.1%, compared to the control group anammox system at C/N = 2:1. Functional gene indicated that it might be a nitrate reducing bacterium.This study shows that the nitrate reduction rate achieved by the Bacillus velezensis M3-1 can be high enough for removing nitrate produced by anammox process, which would enable improve nitrogen removal from wastewater.

Microbial entropy change and external dissipation process of urban sewer ecosystem

As the initial stage of the sewage treatment system, the degradation of pollutants inevitably involves an entropy change process. Microorganisms play a vital role, where they interact with pollutants and constantly adjust own ecosystem. However, there is a lack of research on the entropy change and external dissipation processes within the sewer system. In this study, considering the characteristics of microbial population changes in the biofilm within the urban sewage pipe network, entropy theory is applied to characterize the attributes of different microorganisms. Through revealing the entropy change of the microbial population and chemical composition, a coupling relationship between the functional bacteria diversity, organic substances composition, and external dissipation in the pipeline network is proposed. The results show that the changes of nutrient availability, microbial community structure, and environmental conditions all affect the changes of information entropy in the sewer network. This study is critical for assessing the understanding of ecological dynamics and energy flows within these systems and can help researchers and operation managers develop strategies to optimize wastewater treatment processes, mitigate environmental impacts, and promote sustainable management practices.

Recent advances of partial anammox by controlling nitrite supply in mainstream wastewater treatment through step-feed mode

At present, the step-feed process is a very active branch in practical application of mainstream wastewater treatment, and the anammox technology empowers the sustainable development and in-depth research of step-feed process. This review provides a systematically inspection of the realization and application of partial anammox process through step-feed mode, with a particular focus on controlling nitrite supply for anammox. The characteristics and advantages of step-feed mode in traditional management are reviewed. The unique organics utilization strategy by step-feed and indispensable intermittent aeration mode creates advantages for achieving nitritation (NH4+ → NO2-) and denitratation (NO3- → NO2-), providing flexible combination possibility with anammox. Additionally, the lab- or pilot-scale control strategies with different forms of anammox, including nitritation/anammox, denitratation/anammox, and double-anammox (combined nitritation/anammox and denitratation/anammox), are summarized. Finally, future directions and application perspectives on leveraging the relationship between flocs and biofilm, nitritation and denitratation, and different strains to maximize the anammox proportion in N-removal are proposed.

A Nitrate-Sensing Domain-Containing Chemoreceptor Is Required for Successful Entry and Virulence of Dickeya dadantii 3937 in Potato Plants

Nitrate metabolism plays an important role in bacterial physiology. During the interaction of plant-pathogenic bacteria with their hosts, bacteria face variable conditions with respect to nitrate availability. Perception mechanisms through the chemosensory pathway drive the entry and control the colonization of the plant host in phytopathogenic bacteria. In this work, the identification and characterization of the nitrate- and nitrite-sensing (NIT) domain-containing chemoreceptor of Dickeya dadantii 3937 (Dd3937) allowed us to unveil the key role of nitrate sensing not only for the entry into the plant apoplast through wounds but also for infection success. We determined the specificity of this chemoreceptor to bind nitrate and nitrite, with a slight ligand preference for nitrate. Gene expression analysis showed that nitrate perception controls not only the expression of nitrate reductase genes involved in respiratory and assimilatory metabolic processes but also the expression of gyrA, hrpN, and bgxA, three well-known virulence determinants in Dd3937.

Assessment of a novel microalgae-cork based technology for removing antibiotics, pesticides and nitrates from groundwater

Groundwater pollution has increased in recent years due to the intensification of agricultural and livestock activities. This results in a significant reduction in available freshwater resources. Here, we have studied the long term assessment of a green technology (1-4 L/day) based on a photobioreactor (PBR) containing immobilised microalgae-bacteria in polyurethane foam (PF) followed by a cork filter (CF) for removing nitrates, pesticides (atrazine and bromacil), and antibiotics (sulfamethoxazole and sulfacetamide) from groundwater. The prototype was moderately effective for removing nitrates (58%) at an HRT of 8 days, while its efficiency decreased at a HRT of 4 and 2 days (<20% removal). The combined use of PBR-CF enabled antibiotics and pesticides to be attenuated by up to 95% at an HRT of 8 days, but their attenuation decreased with shorter HRT, with pesticides being the compounds most affected (reducing from 97 to 98% at an HRT of 8 days to 23-45% at an HRT of 2 days). Pesticide transformation products were identified after the CF, supporting biodegradation as the main attenuation process. A gene-based metataxonomic assessment linked the attenuation of micropollutants to the presence of specific pesticide biodegradation species (e.g. genus Phenylobacterium, Sphingomonadaceae, and Caulobacteraceae). Therefore, the results highlighted the potential use of microalgae and cork to treat polluted groundwater.

DNA-based stable isotope probing deciphered the active denitrifying bacteria and triclosan-degrading bacteria participating in granule-based partial denitrification process under triclosan pressure

Granule-based partial denitrification (PD) is a technology that can supply stable nitrite for applying anaerobic ammonia oxidation in wastewater treatment, and triclosan (TCS) is a frequently detected antibacterial agent in wastewater treatment plants, therefore it is possible that TCS could enter into wastewater that is treated using PD technology. However, the active microorganisms responsible for PD and TCS removing in granule-based PD system have not been clearly identified and it is currently not clear how TCS affects the PD process. In this study, the impacts of TCS on PD performance, PD microbial community, antibiotic resistance genes (ARGs), active PD bacteria and TCS-degrading bacteria in a granule-based PD system were investigated. 3 mg/L TCS had adverse influence on PD process, but PD system could recover gradually after inhibiting of 10 days. After a period of domestication, PD granular sludge could achieve 10.66% of TCS degradation efficiency and 43.62% of TCS adsorption efficiency. Microbes might increase their resistance to TCS by increasing the secretion of extracellular polymeric substances, and the secretion of protein might play a more pivotal role than the secretion of polysaccharides in resisting TCS. The short-term shock of TCS might cause the propagation of acrA-03, while the long-term operation of TCS could propagate fabK and intI1. DNA stable isotope probing assay indicated that Thauera was active PD bacteria and TCS-degrading bacteria in the granule-based PD system, and it could contribute to nitrite accumulation and TCS degradation, simultaneously.

Recent advances in partial denitrification-anaerobic ammonium oxidation process for mainstream municipal wastewater treatment

To solve the bottleneck of the unstable accumulation of nitrite in the partial nitrification (PN)-anammox (AMX) in municipal wastewater treatment, a novel process called partial denitrification (PD)-AMX has been developed. PD-AMX, which is known for cost-efficiency and environmental friendliness, has currently exhibited a promising potential for the removal of biological nitrogen from municipal wastewater and has attracted much research interest regarding its process mechanisms, as well as its practical applications. Here, we review the recent advances in the PD process and its coupling to the anammox process, including the development, basic principles, main characteristics, and critical process parameters of the stable operation of the PD-AMX process. We also explore the microbial community and its characteristics in the system and summarize the knowledge of the dominant bacteria to clarify the key factors affecting PD-AMX. Then, we introduce the engineering feasibility and economic feasibility as well as the potential challenges of the process. The induction and implementation of partial denitrification and maintenance of mainstream anammox are critical issues to be urgently solved. Meanwhile, the implementation of a full mainstream anammox application remains burdensome, while the mechanism of partial denitrification coupled to anammox needs to be further studied. Additionally, stable operation performance and process control¹ methods need to be optimized or developed for the PD-AMX system for better engineering practice. This review can help to accelerate the research and application of the PD-AMX process for municipal wastewater treatment.

Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O2 levels

Aerobic methane (CH₄) oxidation coupled to denitrification (AME-D) can not only mitigate CH₄ emission into the atmosphere, but also potentially alleviate nitrogen pollution in surface waters and engineered ecosystems, and it has attracted substantial research interest. O₂ concentration plays a key role in AME-D, yet little is understood about how it impacts microbial interactions. Here, we applied isotopically labeled K¹⁵NO₃ and ¹³CH₄ and metagenomic analyses to investigate the metabolic and microbial link of AME-D at different O₂ levels. Among the four experimental O₂ levels of 21%,10%, 5% and 2.5% and a CH₄ concentration of 8% (i.e., the O₂/CH₄ ratios of 2.62, 1.26, 0.63 and 0.31), the highest NO₃^--N removal occurred in the AME-D system incubated at the O₂ concentration of 10%. Methanol and acetate may serve as the trophic linkage between aerobic methanotrophs and denitrifers in the AME-D systems. Methylotrophs including Methylophilus, Methylovorus, Methyloversatilis and Methylotenera were abundant under the O₂-sufficient condition with the O₂ concentration of 21%, while denitrifiers such as Azoarcus, Thauera and Thiobacillus dominated in the O₂-limited environment with the O₂ concentration of 10%. The competition of denitrifiers and methylotrophs in the AME-D system for CH₄-derived carbon, such as methanol and acetate, might be influenced by chemotactic responses. More methane-derived carbon flowed into methylotrophs under the O₂-sufficient condition, while more methane-derived carbon was used for denitrification in the O₂-limited environment. These findings can aid in evaluating the distribution and contribution of AME-D and in developing strategies for mitigating CH₄ emission and nitrogen pollution in natural and engineered ecosystems.

Nitrogen removal and microbial community diversity in single-chamber electroactive biofilm reactors with different ratios of the cathode surface area to reactor volume

Removal of nitrogen compounds is particularly important domestic wastewater treatment. Our recent study reported the successful removal of nitrogen in single-chamber electroactive biofilm reactors (EBRs) under aeration-free conditions. We hypothesized that the oxygen diffused from the air-cathode is a key factor in the removal of nitrogen in the EBR. If so, the effect of the penetrated oxygen would vary according to the ratio of the air-cathode surface area to the reactor volume (AV ratio) and the hydraulic retention time (HRT). In this study, single-chamber EBRs with three different AV ratios: 125 m²/m³ (EBR-125), 250 m²/m³ (EBR-250), and 500 m²/m³ (EBR-500) were evaluated for the removal of nitrogen under different HRTs of 0.5-6 h. The higher the AV ratio, the greater the increase in nitrification. The total nitrogen (TN) removal efficiency of EBR-125 and EBR-250 decreased as the HRT decreased, while that of EBR-500 increased. EBR-250 showed the highest TN removal (62.0%) with well-balanced nitrification (83.9%) and denitrification (75.1%) at an HRT of 6 h. However, EBR-500 appeared to be superior for practical application because it showed a comparable TN removal (59%) at a substantially short HRT of 1 h. The microbial communities that were involved in the nitrogen cycle varied according to whether the biofilms were located on the anodes, separators, and cathodes but were similar among EBRs with different AV ratios. Nitrifying bacteria were detected in the biofilms that were presented on the cathodes (approximately 7.8% of the total phylotypes), while denitrifying bacteria were mainly found in biofilm that were located on the anodes (approximately 23.3%). Anammox bacteria were also detected on the anode (approximately 3.7%) and in the separator biofilms (approximately 1.9%) of all the EBRs. These results suggest that both the A/V ratio and the HRT could affect the counter diffusion of substrates (NH₄⁺ and organic compounds) and oxygen in the biofilms and allow interactions between a diversity of microorganisms for the successful removal of nitrogen in EBRs. These findings are expected to aid in the development of new applications using EBR for energy-saving wastewater treatment.

Sensing of O2 and nitrate by bacteria: alternative strategies for transcriptional regulation of nitrate respiration by O2 and nitrate

Many bacteria are able to use O₂ and nitrate as alternative electron acceptors for respiration. Strategies for regulation in response to O₂ and nitrate can vary considerably. In the paradigmatic system of E. coli (and γ-proteobacteria), regulation by O₂ and nitrate is established by the O₂ -sensor FNR and the two-component system NarX-NarL (for nitrate regulation). Expression of narGHJI is regulated by the binding of FNR and NarL to the promoter. A similar strategy by individual regulation in response to O₂ and nitrate is verified in many genera by the use of various types of regulators. Otherwise, in the soil bacteria Bacillus subtilis (Firmicutes) and Streptomyces (Actinobacteria), nitrate respiration is subject to anaerobic induction, without direct nitrate induction. In contrast, the NreA-NreB-NreC two-component system of Staphylococcus (Firmicutes) performs joint sensing of O₂ and nitrate by interacting O₂ and nitrate sensors. The O₂ -sensor NreB phosphorylates the response regulator NreC to activate narGHJI expression. NreC-P transmits the signal for anaerobiosis to the promoter. The nitrate sensor NreA modulates NreB function by converting NreB in the absence of nitrate from the kinase to a phosphatase that dephosphorylates NreC-P. Thus, widely different strategies for coordinating the response to O₂ and nitrate have evolved in bacteria.

Recent advances in controlling denitritation for achieving denitratation/anammox in mainstream wastewater treatment plants

Denitratation (NO₃^-→NO₂^-)/anammox is a promising method for anammox application in mainstream wastewater treatment plants (WWTPs) to reduce oxygen and organic matter consumption. Achieving nitrite production via denitratation and controlling denitritation (NO₂^-→N₂) is the basis of the denitratation/anammox process. To control denitritation, the denitrifying biocommunity and growth rate are critically reviewed for biocommunity optimization. Then, the short-term and long-term effects of pH on denitritation were summarized and the possible mechanism was discussed, along with the effect of C/N ratio and organic matter type on denitritation. Meanwhile, the strategies for producing nitrite via controlling denitritation are discussed, as well as the processes for achieving nitrogen removal via denitratation/anammox in WWTPs. Finally, the practical application of denitratation/anammox in a full-scale mainstream WWTP is documented.

The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN

Chemotaxis and energy taxis permit directed bacterial movements in gradients of environmental cues. Nitrate is a final electron acceptor for anaerobic respiration and can also serve as a nitrogen source for aerobic growth. Previous studies indicated that bacterial nitrate taxis is mediated by energy taxis mechanisms, which are based on the cytosolic detection of consequences of nitrate metabolism. Here we show that Pseudomonas aeruginosa PAO1 mediates nitrate chemotaxis on the basis of specific nitrate sensing by the periplasmic PilJ domain of the PA2788/McpN chemoreceptor. The presence of nitrate reduced mcpN transcript levels, and McpN-mediated taxis occurred only under nitrate starvation conditions. In contrast to the NarX and NarQ sensor kinases, McpN bound nitrate specifically and showed no affinity for other ligands such as nitrite. We report the three-dimensional structure of the McpN ligand binding domain (LBD) at 1.3-Å resolution in complex with nitrate. Although structurally similar to 4-helix bundle domains, the ligand binding mode differs since a single nitrate molecule is bound to a site on the dimer symmetry axis. As for 4-helix bundle domains, ligand binding stabilized the McpN-LBD dimer. McpN homologues showed a wide phylogenetic distribution, indicating that nitrate chemotaxis is a widespread phenotype. These homologues were particularly abundant in bacteria that couple sulfide/sulfur oxidation with nitrate reduction. This work expands the range of known chemotaxis effectors and forms the basis for the exploration of nitrate chemotaxis in other bacteria and for the study of its physiological role.IMPORTANCE Nitrate is of central importance in bacterial physiology. Previous studies indicated that movements toward nitrate are due to energy taxis, which is based on the cytosolic sensing of consequences of nitrate metabolism. Here we present the first report on nitrate chemotaxis. This process is initiated by specific nitrate binding to the periplasmic ligand binding domain (LBD) of McpN. Nitrate chemotaxis is highly regulated and occurred only under nitrate starvation conditions, which is helpful information to explore nitrate chemotaxis in other bacteria. We present the three-dimensional structure of the McpN-LBD in complex with nitrate, which is the first structure of a chemoreceptor PilJ-type domain. This structure reveals striking similarities to that of the abundant 4-helix bundle domain but employs a different sensing mechanism. Since McpN homologues show a wide phylogenetic distribution, nitrate chemotaxis is likely a widespread phenomenon with importance for the life cycle of ecologically diverse bacteria.

The Pseudomonas syringae pv. actinidiae chemoreceptor protein F (PscF) periplasmic sensor domain: cloning, purification and X-ray crystallographic analysis

Nitrate- and nitrite-sensing (NIT) domains are found associated with a wide variety of bacterial receptors, including chemoreceptors. However, the structure of a chemoreceptor-associated NIT domain has not yet been characterized. Recently, a chemoreceptor named PscF was identified from the plant pathogen Pseudomonas syringae pv. actinidiae that is predicted to contain a periplasmic NIT domain. The PscF sensor domain (PscF-SD; residues 42-332) was cloned into an appropriate expression vector, recombinantly produced in Escherichia coli BL21-Gold(DE3) cells and purified via immobilized metal-affinity and size-exclusion chromatography. Purified PscF-SD was screened for crystallization; the best crystal diffracted to a maximum resolution of 1.46 Å in space group P212121. However, the data could not be phased using the only available NIT-domain structure (Klebsiella oxytoca NasR; PDB entry 4akk) as the search model. Therefore, a data set from a selenomethionine-labelled protein crystal was also collected. The selenomethionine-labelled protein crystal diffracted to a resolution of 2.46 Å in space group P212121. These data will be used to attempt to solve the structure using the single-wavelength anomalous diffraction technique. The structure is expected to provide insights into the ligand specificity of NIT domains and the role of NIT domains in chemotaxis.

Biological nitrogen removal from sewage via anammox: Recent advances

Biological nitrogen removal from sewage via anammox is a promising and feasible technology to make sewage treatment energy-neutral or energy-positive. Good retention of anammox bacteria is the premise of achieving sewage treatment via anammox. Therefore the anammox metabolism and its factors were critically reviewed so as to form biofilm/granules for retaining anammox bacteria. A stable supply of nitrite for anammox bacteria is a real bottleneck for applying anammox in sewage treatment. Nitritation and partial-denitrification are two promising methods of offering nitrite. As such, the strategies for achieving nitritation in sewage treatment were summarized by reviewing the factors affecting nitrite oxidation bacteria growth. Meanwhile, the methods of achieving partial-denitrification have been developed through understanding the microorganisms related with nitrite accumulation and their factors. Furthermore, two cases of applying anammox in the mainstream sewage treatment plants were documented.

Role of norEF in denitrification, elucidated by physiological experiments with Rhodobacter sphaeroides

Many denitrifying organisms contain the norEF gene cluster, which codes for two proteins that are thought to be involved in denitrification because they are expressed during the reduction of nitrite and nitric oxide. The products of both genes are predicted to be membrane associated, and the norE product is a member of the cytochrome c oxidase subunit III family. However, the specific role of norEF is unknown. The denitrification phenotypes of Rhodobacter sphaeroides strains with and without norEF genes were studied, and it was found that loss of norEF lowered the rate of denitrification from nitrate and resulted in accumulation of micromolar concentrations of nitric oxide during denitrification from nitrite. norEF appears to have no direct role in the reduction of nitric oxide; however, since deletion of norEF in the wild-type 2.4.3 strain had essentially no influence on the kinetics of potential nitric oxide reduction (Vmax and Ks), as measured by monitoring the depletion of a bolus of nitric oxide injected into anoxic cultures without any other electron acceptors. However, norEF-deficient cells that had undergone a more chronic exposure to micromolar concentrations of nitric oxide showed an ∼50% reduction in Vmax but no change in apparent Ks. These results can explain the occurrence of norEF in the 2.4.3 strain of R. sphaeroides, which can reduce nitrate to nitrous oxide, and their absence from strains such as 2.4.1, which likely use nitric oxide reductase to mitigate stress due to episodic exposure to nitric oxide from exogenous sources.

Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell

The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m⁻³ NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m⁻³ NCC in the case of nitrite. Contrarily, nitrous oxide (N₂O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N₂O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N₂O accumulation.

Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients

Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes.

Three types of taxis used in the response of Acidovorax sp. strain JS42 to 2-nitrotoluene

Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer.

Effect of treatment with probiotics as water additives on tilapia (Oreochromis niloticus) growth performance and immune response

A feeding trial was conducted for 40 days to delineate the effect of treatment with probiotics as water additives on tilapia (Oreochromis niloticus) growth performance and immune response. About 360 juveniles were randomly distributed into four treatment groups, each with three replicates. Different probiotics (T-1, Bacillus subtilis B10; T-2, Bacillus coagulans B16; T-3, Rhodopseudomonas palustris G06) were added to the water of tanks at final concentration of 1 x 10(7) cfu ml(-1) every 2 days, with no probiotic added to control tanks. At the end of the feeding trial, fish treated with B. coagulans B16 (T-2) and R. palustris G06 (T-3) had significantly (P < 0.05) higher final weight, daily weight gain, and specific growth rate compared with those treated with B. subtilis B10 (T-1) and those without probiotics (control). The highest (P < 0.05) content of total serum protein was found in T-2 compared with that in T-1, T-3, and the control. However, albumin concentration and albumin/globulin ratio were not affected by the probiotics treatments. Compared with the control, probiotic supplementation remarkably improved activities of superoxide dismutase and catalase (P < 0.05). T-2 fish exhibited higher average myeloperoxidase activity than the control, T-1, and T-3 groups. Regarding serum lysozyme content in tilapia, assays showed no difference (P > 0.05) among the treatment groups. Furthermore, probiotics treatments remarkably increased respiratory burst activity compared with control, with T-2 showing higher values than T-1 and T-3. This indicated that treatment with probiotics, B. coagulans B16 and R. palustris G06, as water additives could be used to enhance immune and health status, thereby improving growth performance of O. niloticus.

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

In anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. Most-probable-number (MPN) dilution series with samples from two freshwater sites yielded only low numbers (≤3×103 cm−3) of phototrophic nitrite oxidizers. Slightly higher numbers (about 104 cm−3) were found in activated sewage sludge. Anaerobic phototrophic oxidation of nitrite was studied with two different isolates, the phototrophic sulfur bacterium strain KS1 and the purple nonsulfur bacterium strain LQ17, both of which were isolated from activated sludge collected from the municipal sewage treatment plant in Konstanz, Germany. Strain KS1 converted 1 mM nitrite stoichiometrically to nitrate with concomitant formation of cell matter within 2–3 days, whereas strain LQ17 oxidized only up to 60 % of the given nitrite to nitrate within several months with the concomitant formation of cell biomass. Nitrite oxidation to nitrate was strictly light-dependent and required the presence of molybdenum in the medium. Nitrite was oxidized in both the presence and absence of oxygen. Nitrite inhibited growth at concentrations higher than 2 mM. Hydroxylamine and hydrazine were found to be toxic to the phototrophs in the range 5–50 μM and did not stimulate phototrophic growth. Based on morphology, substrate-utilization pattern, in vivo absorption spectra, and 16S rRNA gene sequence similarity, strain KS1 was assigned to the genus Thiocapsa and strain LQ17 to the genus Rhodopseudomonas. Also, Thiocapsa roseopersicina strains DSM 217 and DSM 221 were found to oxidize nitrite to nitrate with concomitant growth. We conclude that the ability to use nitrite phototrophically as electron donor is widespread in nature, but low MPN counts indicate that its contribution to nitrite oxidation in the studied habitats is rather limited.

Bacterial energy taxis: a global strategy?

A functional energy metabolism is one of the most important requirements for survival of all kinds of organisms including bacteria. Therefore, many bacteria actively seek conditions of optimal metabolic activity, a behaviour which can be termed "energy taxis". Motility, combined with the sensory perception of the internal energetic conditions, is prerequisite for tactic responses to different energy levels and metabolic yields. Diverse mechanisms of energy sensing and tactic response have evolved among various bacteria. Many of the known energy taxis sensors group among the methyl-accepting chemotaxis protein (MCP)-like sensors. This review summarizes recent advances in the field of energy taxis and explores the current concept that energy taxis is an important part of the bacterial behavioural repertoire in order to navigate towards more favourable metabolic niches and to survive in a specific habitat.

Identification, functional studies, and genomic comparisons of new members of the NnrR regulon in Rhodobacter sphaeroides

Analysis of the Rhodobacter sphaeroides 2.4.3 genome revealed four previously unidentified sequences similar to the binding site of the transcriptional regulator NnrR. Expression studies demonstrated that three of these sequences are within the promoters of genes, designated paz, norEF, and cdgA, in the NnrR regulon, while the status of the fourth sequence, within the tat operon promoter, remains uncertain. nnrV, under control of a previously identified NnrR site, was also identified. paz encodes a pseudoazurin that is a donor of electrons to nitrite reductase. paz inactivation did not decrease nitrite reductase activity, but loss of pseudoazurin and cytochrome c(2) together reduced nitrite reduction. Inactivation of norEF reduced nitrite and nitric oxide reductase activity and increased the sensitivity to nitrite in a taxis assay. This suggests that loss of norEF increases NO production as a result of decreased nitric oxide reductase activity. 2.4.3 is the only strain of R. sphaeroides with norEF, even though all four of the strains whose genomes have been sequenced have the norCBQD operon and nnrR. norEF was shown to provide resistance to nitrite when it was mobilized into R. sphaeroides strain 2.4.1 containing nirK. Inactivation of the other identified genes did not reveal any detectable denitrification-related phenotype. The distribution of members of the NnrR regulon in R. sphaeroides revealed patterns of coselection of structural genes with the ancillary genes identified here. The strong coselection of these genes indicates their functional importance under real-world conditions, even though inactivation of the majority of them does not impact denitrification under laboratory conditions.

Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors

The response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. The observed response was species-specific, dependent on the prior growth conditions, and was inhibited by oxygen. We observed attraction toward nitrate when Dechloromonas aromatica strain RCB and Azospira suillum strain PS were grown with nitrate. When D. aromatica and Dechloromonas agitata strain CKB were grown with perchlorate, both responded to nitrate, chlorate, and perchlorate. When A. suillum was grown with perchlorate, the organism responded to chlorate and perchlorate but not nitrate. A gene replacement mutant in the perchlorate reductase subunit (pcrA) of D. aromatica resulted in a loss of the attraction response toward perchlorate but had no impact on the nitrate response. Washed-cell suspension studies revealed that the perchlorate grown cells of D. aromatica reduced both perchlorate and nitrate, while A. suillum cells reduced perchlorate only. Based on these observations, energy taxis was proposed as the underlying mechanism for the responses to (per)chlorate by D. aromatica. To the best of our knowledge, this study represents the first investigation of the response behavior of perchlorate-reducing bacteria to environmental stimuli. It clearly demonstrates attraction toward chlorine oxyanions and the unique ability of these organisms to distinguish structurally analogous compounds, nitrate, chlorate, and perchlorate and respond accordingly.

Feed formulations to reduce N excretion and ammonia emission from poultry manure

This summary focuses on reducing nitrogen (N) and ammonia emissions from poultry manure through the use of improved amino acid digestibilities and enzyme supplementation. Proper feed processing techniques, phase feeding, and the minimization of feed and water waste can contribute to additional minor reductions in these emissions. Reductions in environmental pollution can be achieved through improved diet formulation based on available nutrients in the ingredients, reducing crude protein (CP) levels and adding synthetic amino acids. Use of amino acid and CP digestibilities can reduce N excretion up to 40% and a 25% increase in N digestibility can be achieved with enzyme supplementation in broiler diets. Digestibilities can be measured by two methods: the excreta and ileal amino acid digestibilities. Both methods allow amino acid levels to be reduced by 10% or more. Enzyme supplementation decreases intestinal viscosity, improves metabolizable energy levels, and increases amino acid digestibilities. Many feed manufacturers still use total amino acid content to formulate feeds. To meet amino acid requirements, crystalline amino acids are needed. The use of feather, meat and bone meal must not be overestimated or underestimated and the limiting amino acids such as cystine, tryptophan, and threonine must be carefully analyzed.

Cyanobacterial chemotaxis to extracts of host and nonhost plants

Chemotaxis may be important when forming cyanobacterial symbioses. However, knowledge of cyanobacterial attraction towards plants and factors affecting chemotaxis is limited. Chemo-attraction was observed in Nostoc strains 8964:3 and PCC 73102 towards exudate or crushed extract of the natural hosts Gunnera manicata, Cycas revoluta and Blasia pusilla, and the nonhost plants Trifolium repens, Arabidopsis thaliana and Oryza sativa. As all tested plant extracts generated chemotaxis, the possibility to attract cyanobacteria may be widespread in plants. Chemotaxis was reduced by increased temperature and darkness and was stimulated by phosphorous and iron starvation and elevated salt concentration. Sugars (arabinose, galactose, and glucose) had a positive effect on chemotaxis, whereas flavonoids (chrysin and naringenin) and amino acids (methionine, glycine, serine, phenylalanine, glutamine, and lysine) had no effect.

Expression of nitrite and nitric oxide reductases in free-living and plant-associated Agrobacterium tumefaciens C58 cells

A number of the bacteria that form associations with plants are denitrifiers. To learn more about how the association with plants affects expression of denitrification genes, the regulation of nitrite and nitric oxide reductases was investigated in Agrobacterium tumefaciens. Analysis of free-living cells revealed that expression of the genes encoding nitrite and nitric oxide reductases, nirK and nor, respectively, requires low-oxygen conditions, nitric oxide, and the transcriptional regulator NnrR. Expression of nor was monitored in plant-associated bacteria using nor-gfp fusion expression. In root association experiments, only a small percentage of the attached cells were fluorescent, even when they were incubated under a nitrogen atmosphere. Inactivation of nirK had no significant effect on the ability of A. tumefaciens to bind to plant roots regardless of the oxygen tension, but it did decrease the occurrence of root-associated fluorescent cells. When wild-type cells containing the gfp fusion were infiltrated into leaves, most cells eventually became fluorescent. The same result was obtained when a nirK mutant was used, suggesting that nitric oxide activated nor expression in the endophytic bacteria. Addition of a nitric oxide synthase inhibitor to block nitric oxide generation by the plant prevented gfp expression in infiltrated nitrite reductase mutants, demonstrating that plant-derived nitric oxide can activate nor expression in infiltrated cells.

Ecological role of energy taxis in microorganisms

Motile microorganisms rapidly respond to changes in various physico-chemical gradients by directing their motility to more favorable surroundings. Energy generation is one of the most important parameters for the survival of microorganisms in their environment. Therefore it is not surprising that microorganisms are able to monitor changes in the cellular energy generating processes. The signal for this behavioral response, which is called energy taxis, originates within the electron transport system. By coupling energy metabolism and behavior, energy taxis is fine-tuned to the environment a cell finds itself in and allows efficient adaptation to changing conditions that affect cellular energy levels. Thus, energy taxis provides cells with a versatile sensory system that enables them to navigate to niches where energy generation is optimized. This behavior is likely to govern vertical species stratification and the active migration of motile cells in response to shifting gradients of electron donors and/or acceptors which are observed within microbial mats, sediments and soil pores. Energy taxis has been characterized in several species and might be widespread in the microbial world. Genome sequencing revealed that many microorganisms from aquatic and soil environments possess large numbers of chemoreceptors and are likely to be capable of energy taxis. In contrast, species that have a fewer number of chemoreceptors are often found in specific, confined environments, where relatively constant environmental conditions are expected. Future studies focusing on characterizing behavioral responses in species that are adapted to diverse environmental conditions should unravel the molecular mechanisms underlying sensory behavior in general and energy taxis in particular. Such knowledge is critical to a better understanding of the ecological role of energy taxis.

Agrobacterium tumefaciens twin-arginine-dependent translocation is important for virulence, flagellation, and chemotaxis but not type IV secretion

This study characterized the contribution of the twin-arginine translocation (TAT) pathway to growth, motility, and virulence of the phytopathogen Agrobacterium tumefaciens. In contrast to wild-type strain A348, a tatC null mutant failed to export the green fluorescent protein fused to the trimethylamine N-oxide reductase (TorA) signal sequence or to grow on nitrate as a sole electron acceptor during anaerobic growth. The tatC mutant displayed defects in growth rate and cell division but not in cell viability, and it also released abundant levels of several proteins into the culture supernatant when grown in rich medium or in vir induction minimal medium. Nearly all A348 cells were highly motile in both rich and minimal media. By contrast, approximately 0.1% of the tatC mutant cells were motile in rich medium, and <0.01% were motile in vir induction medium. Nonmotile tatC mutant cells lacked detectable flagella, whereas motile tatC mutant cells collected from the edge of a motility halo possessed flagella but not because of reversion to a functional TAT system. Motile tatC cells failed to exhibit chemotaxis toward sugars under aerobic conditions or towards nitrate under anaerobic conditions. The tatC mutant was highly attenuated for virulence, only occasionally (approximately 15% of inoculations) inciting formation of small tumors on plants after a prolonged incubation period of 6 to 8 weeks. However, an enriched subpopulation of motile tatC mutants exhibited enhanced virulence compared to the nonmotile variants. Finally, the tatC mutant transferred T-DNA and protein effectors to plant cells and a mobilizable IncQ plasmid to agrobacterial recipients at wild-type levels. Together, our findings establish that, in addition to its role in secretion of folded cofactor-bound enzymes functioning in alternative respiration, the TAT system of A. tumefaciens is an important virulence determinant. Furthermore, this secretion pathway contributes to flagellar biogenesis and chemotactic responses but not to sensory perception of plant signals or the assembly of a type IV secretion system.