Discovery of the first light‐dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria

In all photosynthetic organisms, chlorophylls function as light‐absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen‐sensitive dark‐operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen‐insensitive but light‐dependent PORs (LPORs). Based on this observation it was suggested that light‐dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α‐proteobacterium Dinoroseobacter shibae DFL12^T. In vitro and in vivo functional assays unequivocally prove light‐dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence‐based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light‐dependent enzyme of D. shibae DFL12^T might have been obtained from cyanobacteria by horizontal gene transfer.     

Autotrophic, Hydrogen-Oxidizing, Denitrifying Bacteria in Groundwater, Potential Agents for Bioremediation of Nitrate Contamination

Addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (Cape Cod, Mass.). Hydrogen uptake by the core material was immediate and rapid, with an apparent K_m of 0.45 to 0.60 μM and a V_max of 18.7 nmol cm^-3 h^-1 at 30°C. Nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. Eight of the strains grew autotrophically on hydrogen with either oxygen or nitrate as the electron acceptor. One strain grew mixotrophically. All of the isolates were capable of heterotrophic growth, but none were similar to Paracoccus denitrificans, a well-characterized hydrogen-oxidizing denitrifier. The kinetics for hydrogen uptake during denitrification were determined for each isolate with substrate depletion progress curves; the K_ms ranged from 0.30 to 3.32 μM, with V_maxs of 1.85 to 13.29 fmol cell^-1 h^-1. Because these organisms appear to be common constituents of the in situ population of the aquifer, produce innocuous end products, and could be manipulated to sequentially consume oxygen and then nitrate when both were present, these results suggest that these organisms may have significant potential for in situ bioremediation of nitrate contamination in groundwater.     

Nitrate and nitrite in interstitial waters of eelgrass beds in relation to the rhizosphere

The distribution of nitrate and nitrite in the interstitial water of the sediment of eelgrass (Zostera marina) bed of Izembek Lagoon, Alaska, were investigated. Their concentrations were relatively high (0 to 9.8 μg-at.N·1^?1, average 4.8 for nitrate; 0 to 4.0 μ-at.N·1^?1, average 1.9 for nitrite) although the sediments were anoxic and contained hydrogen sulphide. The rates of bacterial denitrification measured by ¹⁵N tracer technique ranged from 0.49×10^?10 to 1.2 × 10^?9 g-atN·g^?1·h^?1. When a steady state is maintained, the loss of nitrate and nitrite must be balanced by their production by bacterial nitrification. Experimentally determined rate of nitrification in the sediment was of the same order. A model experiment demonstrated that oxygen is transported from leaves to rhizomes and roots of eelgrass and released into the sediment. The oxygen is used for nitrification in the rhizosphere in anoxic sediments.     

Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2(-) and O2 concentrations.

The oxygen control of denitrification and its emission of NO/N2O/N2 was investigated by incubation of Nycodenz-extracted soil bacteria in an incubation robot which monitors O2, NO, N2O and N2 concentrations (in He+O2 atmosphere). Two consecutive incubations were undertaken to determine (1) the regulation of denitrification by O2 and NO2(-) during respiratory O2 depletion and (2) the effects of re-exposure to O2 of cultures with fully expressed denitrification proteome. Early denitrification was only detected (as NO and N2O) at 相似文献   

Interactions between respiration and denitrification during growth of Thiosphaera pantotropha in continuous culture

Abstract The effects of oxygen on the use of nitrate as an electron acceptor by the denitrifying bacterium Thiosphaera pantotropha were investigated during growth on acetate. In batch cultures under aerobic conditions nitrate was not utilised and the growth rate constant was 0.55 h⁻¹. The corresponding value for growth on nitrate under anoxic conditions was 0.37 h⁻¹. In acetate-limited continuous cultures with feedback control of the dissolved oxygen concentration, nitrate utilisation was totally inhibited by the lowest concentration of oxygen tested (22 μM). Carbon conversion efficiencies with acetate increased from 0.28 with nitrate to 0.44 with oxygen. The rates of nitrification calculated from nitrogen balance studies were not greater than 1.5% of the rate of anoxic denitrification.     

Nitrate depletion in the riparian zone and stream channel of a small headwater catchment

A mass balance procedure was used to determine rates of nitrate depletion in the riparian zone and stream channel of a small New Zealand headwater stream. In all 12 surveys the majority of nitrate loss (56–100%) occurred in riparian organic soils, despite these soils occupying only 12% of the stream's border. This disproportionate role of the organic soils in depleting nitrate was due to two factors. Firstly, they were located at the base of hollows and consequently a disproportionately high percentage (37–81%) of the groundwater flowed through them in its passage to the stream. Secondly, they were anoxic and high in both denitrifying enzyme concentration and available carbon. Direct estimates ofin situ denitrification rate for organic soils near the upslope edge (338 mg N m^–2 h^–1) were much higher than average values estimated for the organic soils as a whole (0.3–2.1 mg N m^–2 h^–1) and suggested that areas of these soils were limited in their denitrification activity by the supply of nitrate. The capacity of these soils to regulate nitrate flux was therefore under-utilized. The majority of stream channel nitrate depletion was apparently due to plant uptake, with estimates of thein situ denitrification rate of stream sediments being less than 15% of the stream channel nitrate depletion rate estimated by mass balance.This study has shown that catchment hydrology can interact in a variety of ways with the biological processes responsible for nitrate depletion in riparian and stream ecosystems thereby having a strong influence on nitrate flux. This reinforces the view that those seeking to understand the functioning of these ecosystems need to consider hydrological phenomena.     

Light Enhances Survival of Dinoroseobacter shibae during Long-Term Starvation

Aerobic anoxygenic phototrophs (AAPs) as being photoheterotrophs require organic substrates for growth and use light as a supplementary energy source under oxic conditions. We hypothesized that AAPs benefit from light particularly under carbon and electron donor limitation. The effect of light was determined in long-term starvation experiments with Dinoroseobacter shibae DFL 12^T in both complex marine broth and defined minimal medium with succinate as the sole carbon source. The cells were starved over six months under three conditions: continuous darkness (DD), continuous light (LL), and light/dark cycle (LD, 12 h/12 h, 12 µmol photons m⁻² s⁻¹). LD starvation at low light intensity resulted in 10-fold higher total cell and viable counts, and higher bacteriochlorophyll a and polyhydroxyalkanoate contents. This coincided with better physiological fitness as determined by respiration rates, proton translocation and ATP concentrations. In contrast, LD starvation at high light intensity (>22 µmol photons m⁻² s⁻¹, LD conditions) resulted in decreasing cell survival rates but increasing carotenoid concentrations, indicating a photo-protective response. Cells grown in complex medium survived longer starvation (more than 20 weeks) than those grown in minimal medium. Our experiments show that D. shibae benefits from the light and dark cycle, particularly during starvation.     

Nitrate reduction by Citrobacter diversus under aerobic environment

A new aerobic denitrifier, Citrobacter diversus, was isolated from both nitrification and denitrification sludge. To monitor the variation in the concentration of nitrogen oxides, aerobic denitrification by C. diversus was carried out in a batch reactor. When the nitrate concentration was greater than 180 mg N l⁻¹, the nitrate reduction rate became stable. The effect of the C/N ratio on the denitrification activity was also investigated. The results showed that the optimum denitrification activity was obtained when the C/N ratio was 4–5. The range of the C/N ratio was higher than that for traditional anoxic denitrification. The effect of the dissolved oxygen concentration was further studied; and it was found that the range of dissolved oxygen concentrations, both for specific growth rates and for specific denitrification rates, was 2–6 mg⁻¹. From these results, it can be concluded that both the concentration of dissolved oxygen and the C/N ratio are key factors in the aerobic denitrification by C. diversus. Received: 23 November 1999 / Received revision: 4 February 2000 / Accepted: 13 February 2000     

Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying,hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment

Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis within Epsilonproteobacteria, which is involved in marine sedimentary sulfur oxidation and denitrification. Strain AST-10^T (= DSM 22096^T = JCM 18418^T) was isolated from the coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong. It grew chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole electron donor and nitrate as the electron acceptor under anoxic conditions. It was rod-shaped and grew at 15-35°C (optimum at 30°C), pH 6.5-8.5 (optimum at 7.0-7.5), and 10-60 g L^-1 NaCl (optimum at 30 g L^-1). Genome sequencing and annotation of strain AST-10^T showed a 2,302,023 bp genome size, with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3 rRNA genes.     

Biological treatment of low-salinity shrimp aquaculture wastewater using sequencing batch reactor

In order to improve the water quality in shrimp aquaculture operated under low-salinity conditions, a sequencing batch reactor (SBR) was tested for treatment of the wastewater. This water from the backwash of a single-bead filter from the Waddell Mariculture Center, South Carolina, contained high concentrations of carbon and nitrogen and was successfully treated using the SBR. By operating the reactor sequentially in aerobic, anoxic and aerobic modes, nitrification and denitrification were achieved, as well as removal of carbon. Specifically, the initial chemical oxygen demand (COD) concentration of 1201 mg l⁻¹ was reduced to 32 mg l⁻¹ within 8 days of reactor operation. Ammonia in the sludge was nitrified within 3 days. The denitrification of nitrate was achieved by the anoxic process and total removal of nitrate was observed.     

Growth Yields in Bacterial Denitrification and Nitrate Ammonification

Denitrification and nitrate ammonification are considered the highest-energy-yielding respiration systems in anoxic environments after oxygen has been consumed. The corresponding free energy changes are 7 and 35% lower than that of aerobic respiration, respectively. Growth yield determinations with pure cultures of Paracoccus denitrificans and Pseudomonas stutzeri revealed that far less energy is converted via ATP into cell mass than expected from the above calculations. Denitrification with formate or hydrogen as electron donor yielded about 2.4 to 3.0 g dry matter per mol formate or hydrogen and 15 to 18 g dry matter per mol acetate. Similar yields with acetate were obtained with Pseudomonas stutzeri. Wolinella succinogenes and Sulfurospirillum deleyianum, which reduce nitrate to ammonia, both exhibited similar yield values with formate or H₂ plus nitrate. The results indicate that ATP synthesis in denitrification is far lower than expected from the free energy changes and even lower than in nitrate ammonification. The results are discussed against the background of our present understanding of electron flow in denitrification and with respect to the importance of denitrification and nitrate ammonification in the environment.     

The denitrification capacity of sediment from a hypereutrophic lake

SUMMARY.

• 1 In sediment from Wintergreen Lake, Michigan, denitrification was not detectable by the acetylene inhibition method at in situ nitrate concentrations. When nitrate was added to sediment slurries, denitrification capacities up to 18.8μg N g^-1 h^-1 were measured. The denitrification capacities decreased with increasing sediment depth and distance from shore.
• 2 The high denitrification capacities in these sediments which under natural conditions had no supply of nitrate and oxygen suggested that denitrifies with alternative mechanisms for anaerobic energy conversion were present. Nitrous oxide was a significant portion of the N-gas produced immediately after the nitrate addition. Small amounts (4–5% of the total N-gas production) of nitric oxide accumulated in the early phase of nitrate reduction. Presumably after depletion of nitrate and nitrite both N₂O and NO were further reduced to N₂.
• 3 About 70%r of the added nitrate was denitrified, and the remainder was assumed to have been reduced to ammonium.

     

Roseibacterium beibuensis sp. nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

A novel aerobic, bacteriochlorophyll-containing bacteria strain JLT1202r^T was isolated from Beibu Gulf in the South China Sea. Cells were gram-negative, non-motile, and short-ovoid to rod-shaped with two narrower poles. Strain JLT1202r^T formed circular, opaque, wine-red colonies, and grew optimally at 3–4?% NaCl, pH 7.5–8.0 and 28–30?°C. The strain was catalase, oxidase, ONPG, gelatin, and Voges–Proskauer test positive. In vivo absorption spectrum of bacteriochlorophyll a presented two peaks at 800 and 877?nm. The predominant cellular fatty acid was C_18:1 ω7c and significant amounts of C_16:0, C_18:0, C_10:0 3-OH, C_16:0 2-OH, and 11-methyl C_18:1 ω7c were present. Strain JLT1202r^T contained Q-10 as the major respiratory quinone and the genomic DNA G+C content was 76.3?mol%. Phylogenetic analysis based on 16S rRNA gene sequences of various species with validly published names showed that strain JLT1202r^T fell within the genus Roseibacterium, family Rhodobacteraceae, sharing the highest similarity with Roseibacterium elongatum OCh 323^T (97.9?% similarity), followed by Dinoroseobacter shibae DFL 12^T (95.4?% similarity). The phylogenetic distance of pufM genes between strain JLT1202r^T and R. elongatum OCh 323^T was 9.4?%, suggesting that strain JLT1202r^T was distinct from the only strain of the genus Roseibacterium. Based on the variabilities of phylogenetic and phenotypic characteristics, strain JLT1202r^T stands for a novel species of the genus Roseibacterium and the name R. beibuensis sp. nov. is proposed with JLT1202r^T as the type strain (=JCM 18015^T?=?CGMCC 1.10994^T).     

Kinetic Behavior of Some Polyphosphate-Accumulating Bacteria Isolates in the Presence of Nitrate and Oxygen

This paper studies the phosphate uptake by pure cultures of Aeromonas hydrophila, Klebsiella oxytoca, Agrobacterium tumefaciens, and Aquaspirillum dispar in the presence of both nitrate and oxygen. It is shown that species were able to respire both electron acceptors for phosphate accumulation. A. tumefaciens and A. dispar accumulated overall phosphate both in oxic and anoxic culture conditions, whereas A. hydrophila and K. oxytoca eliminated overall phosphate only in oxic conditions. A. dispar was able to remove phosphate by reducing oxygen and nitrate simultaneously with the production of dinitrogen gas. The anoxic denitrification observed in the cultures of adapted and nonadapted cells to nitrate showed that only A. dispar have a denitrification rate superior when the cells were adapted to nitrate. Received: 15 December 1998 / Accepted: 21 January 1999     

Atypical Polyphosphate Accumulation by the Denitrifying Bacterium Paracoccus denitrificans

Polyphosphate accumulation by Paracoccus denitrificans was examined under aerobic, anoxic, and anaerobic conditions. Polyphosphate synthesis by this denitrifier took place with either oxygen or nitrate as the electron acceptor and in the presence of an external carbon source. Cells were capable of poly-β-hydroxybutyrate (PHB) synthesis, but no polyphosphate was produced when PHB-rich cells were incubated under anoxic conditions in the absence of an external carbon source. By comparison of these findings to those with polyphosphate-accumulating organisms thought to be responsible for phosphate removal in activated sludge systems, it is concluded that P. denitrificans is capable of combined phosphate and nitrate removal without the need for alternating anaerobic/aerobic or anaerobic/anoxic switches. Studies on additional denitrifying isolates from a denitrifying fluidized bed reactor suggested that polyphosphate accumulation is widespread among denitrifiers.     

Interactive influences of the marine yabby (<Emphasis Type="Italic">Trypaea australiensis</Emphasis>) and mangrove (<Emphasis Type="Italic">Avicennia marina</Emphasis>) leaf litter on benthic metabolism and nitrogen cycling in sandy estuarine sediment

A previous study has demonstrated that in sandy sediment the marine yabby (Trypaea australiensis) stimulated benthic metabolism, nitrogen regeneration and nitrification, but did not stimulate denitrification, as the intense bioturbation of the yabbies eliminated anoxic microzones amenable to denitrification. It was hypothesised that organic matter additions would alleviate this effect as the buried particles would provide anoxic microniches for denitrifiers. To test this hypothesis a 55-day microcosm (75 cm × 36 cm diameter) experiment, comprising four treatments: sandy sediment (S), sediment + yabbies (S + Y), sediment + A. marina litter (S + OM) and sediment + yabbies + A. marina litter (S + Y + OM), was conducted. Trypaea australiensis significantly stimulated benthic metabolism, nitrogen regeneration, nitrification and nitrate reduction in the presence and the absence of litter additions. In contrast, the effects of litter additions alone were more subtle, developed gradually and were only significant for sediment oxygen demand. However, there was a significant interaction between yabbies and litter with rates of total nitrate reduction and denitrification being significantly greater in the S + Y + OM than all other treatments, presumably due to the decaying buried litter providing anoxic micro-niches suitable to nitrate reduction. In addition, both T. australiensis and litter significantly decreased rates of DNRA and its contribution to nitrate reduction.