Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions.

A moderately thermophilic, aerobic, stalked bacterium (strain MA2T) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MA2T was most closely related to the genera Rhodobium,Parvibaculum, and Rhodoligotrophos (92-93 % similarity) within the class Alphaproteobacteria. Strain MA2T was a Gram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16-48 °C (optimum growth at 42 °C). This strain required yeast extract and NaCl (>1 %, w/v) for growth, tolerated up to 11 % (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The DNA G+C content was 60.7 mol%. Strain MA2T performed denitrification and produced N2O from nitrate under strictly microaerobic conditions. Strain MA2T possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, Tepidicaulis marinus gen. nov., sp. nov., are proposed, with MA2T ( = NBRC 109643T = DSM 27167T) as the type strain of the species.

Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent.

A moderately thermophilic, methanol-oxidizing bacterium (strain Gela4(T)) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4(T) was closely related to members of the genus 'Methyloligella' (94.7% similarity) within the class Alphaproteobacteria. Strain Gela4(T) was a Gram-staining-negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4(T) was 19-43 °C (optimal growth at 35 °C). Strain Gela4(T) tolerated up to 9% NaCl with an optimum at 1%. The organism was a facultative methylotroph that could utilize methanol, methylamine, trimethylamine and a variety of multi-carbon compounds. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63.9 mol%. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Methyloceanibacter caenitepidi is proposed, with Gela4(T) ( = NBRC 109540(T) = DSM 27242(T)) as the type strain.

Distribution and characterization of anammox in a swine wastewater activated sludge facility.

Anaerobic ammonium oxidation (anammox) is a novel biological nitrogen removal process that oxidizes NH4(+) to N2 with NO2(-) as an electron acceptor. The purpose of this study was to examine the potential activity and characteristics of anammox in a conventional swine wastewater treatment facility, which uses an activated sludge system consisting of three cascade aeration tanks equipped with ceramic support material. Anammox activity was estimated by a (15)N tracer assay method and was detected in all the sludge and biofilm samples in each aeration tank. Biofilm taken from the third aeration tank, in which the dissolved oxygen concentration was 7.5 mg/L and the wastewater included a high concentration of NO3(-), showed by far the highest anammox activity. A clone library analysis showed the existence of anammox bacteria closely related to 'Candidatus Jettenia asiatica' and 'Ca. Brocadia caroliniensis'. The optimum conditions for anammox activity were a pH of 6.7-7.2, a temperature of 35 °C, a NO2(-) concentration of 10 mmol/L or less, and an NH4(+) concentration of 32 mmol/L or less.

Detection of anammox activity and 16S rRNA genes in ravine paddy field soil.

An anammox assay involving a ¹5N tracer and gas chromatography-mass spectrometry revealed that the potential anammox activity accounted for 1 to 5% of total N2 production in a ravine paddy field, Japan. Among four 4-cm-deep layers, the top layer showed the highest activity. Clone libraries showed that the DNA in the top layer contained sequences related to those of Candidatus 'Brocadia fulgida', Ca. 'B. anammoxidans', and Ca. 'Kuenenia stuttgartiensis'. These results suggest that a specific population of anammox bacteria was present in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox.

Distribution and diversity of anaerobic ammonium oxidation (anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan.

Although the emission of N(2) via anaerobic ammonium oxidation (anammox) is a key process in the elimination of nitrogenous compounds from aquatic environments, little information is available regarding its significance and the relevant microorganisms (anammox bacteria) in eutrophic freshwater lakes. In the present study, the anammox bacteria in the sediment of a eutrophic lake in Japan, Lake Kitaura, were examined using a (15)N-tracer technique to measure their potential anammox activity. Potential anammox activity was localized to the northern region of the lake where a stable supply of both NH(4)(+) and NO(3)(-) existed in the sediment. These results suggest the contribution of anammox bacteria to the total emission of N(2) from sediment in this eutrophic lake to not be negligible. Moreover, selective PCR successfully amplified anammox bacteria-related (Brocadiales-related) 16S rRNA genes from sediment samples in which potential anammox activity was observed. The clone libraries consisted of diverse phylotypes except the genus "Scalindua"-lineages, and the lineages of genus "Brocadia" were dominantly recovered, followed by the genus "Kuenenia"-lineages. Most of them, however, were novel and phylogenetically distinguishable from known Brocadiales species. A unique population of anammox bacteria inhabits and potentially contributes to the emission of N(2) from Lake Kitaura.

Evidence of exponential growth of an anammox population in an anaerobic batch culture.

Twenty-five replicates of growth medium for anaerobic ammonium oxidation (anammox) containing (15)N-labeled ammonium and non-labeled nitrite were inoculated into an anammox enrichment culture at low density, and anaerobically incubated batchwise. In the headspace, (29)N(2) partial pressure linearly increased via anammox in 25 vials, confirming that anammox populations were viable in all subcultures. On prolonged incubation, exponential increases in (29)N(2) were not observed in all but 13 subcultures, suggesting that the anammox population may not proliferate unless all conditions for growth are satisfied. The estimated first-order rate coefficients in those 13 subcultures varied from 0.0029 to 0.0048 h(-1).

Contribution of anammox bacteria to benthic nitrogen cycling in a mangrove forest and shrimp ponds, Haiphong, Vietnam.

Mangrove forests are common in subtropical regions, and have received considerable attention as vegetative buffers against anthropogenic N-loading. In this study, we investigated anaerobic ammonium oxidation (anammox) as one of potentially important microbial N-removing pathways in mangrove and shrimp pond sediment in Haiphong, Vietnam. Measurements with (15)N-labeled compounds demonstrated the occurrence of anammox in sediment of mangrove forest and a water channel connecting shrimp ponds to the sea in both 2005 and 2007, and of a semi-intensive shrimp pond in 2005. The rate of potential anammox activity reached to 0.7 nmol-N(2) cm(-3) h(-1), although the contribution of anammox was less significant than denitrification. Anammox-type 16S rRNA gene fragments phylogenetically related to 'Scalindua' species were predominantly recovered from mangrove forest and water channel sediment in a PCR-clone library analysis targeting anammox bacteria. 'Kuenenia'-like gene fragments were also recovered from shrimp pond sediment as the major component. We demonstrated the occurrence of potential anammox activity, and suggested the possibility that diverse species of uncultured anammox bacteria contribute to the nitrogen cycle in subtropical mangrove-aquaculture ecosystems. Furthermore, this study provides new insight into the biogeography of anammox bacteria: 'Scalindua' and 'Kuenenia'-like species coexisted in the blackish sediment as in some temperate estuarine sediment.

Rate determination and distribution of anammox activity in activated sludge treating swine wastewater.

This paper presents a quantitative investigation and analysis of anammox activity in sludge taken from biological swine wastewater treatment plants. An incubation experiment using a (15)N tracer technique showed anammox activity in sludge taken from 6 out of 13 plants with the rate ranging from 0.0036 micromol-N(2)/g-VSS/h to 3.1 micromol-N(2)/g-VSS/h, and in a biofilm with the highest activity at 25.8 micromol-N(2)/g-VSS/h. It is notable that 9 out of 11 sludges in which the pH was maintained between 6.6 and 8.1 retained anammox activity, while those with either a lower or higher pH did not. Moreover, anammox-positive sludge had a significantly higher concentration of NO(2)(-)-N plus NO(3)(-)-N than did anammox-negative sludge. A significant difference was not observed between anammox-positive and -negative sludge regarding BOD/NH(4)(+)-N in the influent, DO concentration in aeration tanks, and the concentrations of NH(4)(+)-N, free nitric acid, and free ammonia.

Nitrogen removal by co-occurring methane oxidation, denitrification, aerobic ammonium oxidation, and anammox.

The pathway for removing NO(3)(-) and NH(4)(+) from wastewater in the presence of both CH(4) and O(2) was clarified by studying microbial activity and community. Batch incubation tests were performed to characterize the microbial activity of the sludge, which was acclimatized in a bioreactor in which O(2) and CH(4) were supplied to treat wastewater containing NO(3)(-) and NH(4)(+) . The tests showed that the sludge removed significant amounts of NO(3)(-) and NH(4)(+) in the presence of CH(4) and O(2), and the presence of the activity of methane oxidation, denitrification, nitrification, and anammox in the sludge. It was estimated that the total inorganic nitrogen removal was attributed to denitrification associated with methane oxidation as 53.4%, microbial assimilation as 37.9%, and anammox as 8.7%. Nitrification also contributed to NH(4)(+) decrease as 34.5% and anammox as 6.4%. Anammox activity was unambiguously demonstrated by (29)N(2) production in anaerobic batch incubation with (15)N-labeled inorganic nitrogen compounds. The presence of methane-oxidizing bacteria and candidate denitrifiers in the sludge was shown by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Clone library analysis of the PCR-amplified 16S rRNA gene fragment using specific primers for aerobic ammonium oxidizer and anammox revealed the presence of these bacteria. The results reveal that complex nitrogen-removal processes occur in the presence of CH(4) and O(2) by methanotroph, denitrifier, aerobic ammonium oxidizer, and anammox.

Anaerobic ammonium oxidation (anammox) irreversibly inhibited by methanol.

Methanol inhibition of anaerobic ammonium oxidation (anammox) activity was characterized. An enrichment culture entrapped in a polyethylene glycol gel carrier was designed for practical uses of wastewater treatment. Batch experiments demonstrated that anammox activity decreased with increases in methanol concentration, and relative activity reached to 29% of the maximum when 5 mM methanol was added. Also, batch experiments were conducted using anammox sludge without immobilization. Anammox activity was evaluated by quantifying (14)N(15)N ((29)N) emission by combined gas chromatography-quadrupole mass spectrometry, and the anammox activity was found to be almost as sensitive to methanol as in the earlier trials in which gel carriers were used. These results indicated that methanol inhibition was less severe than previous studies. When methanol was added in the influent of continuous feeding system, relative activity was decreased to 46% after 80 h. Although the addition was halted, afterwards the anammox activity was not resumed in another 19 days of cultivation, suggesting that methanol inhibition to anammox activity was irreversible. It is notable that methanol inhibition was not observed if anammox activity was quiescent when substrate for anammox was not supplied. These results suggest that methanol itself is not inhibitory and may not directly inhibit the anammox activity.

Denitrification activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest.

Denitrification activity and bacterial community constituents were investigated in both well-drained and poorly drained soils of a temperate forest in central Japan by (15)N tracer experiments and a cloning-sequencing approach. Denitrification activity was much higher in wet soil than in dry soil, based on (15)N(15)N ((30)N(2)) and (15)N(15)NO ((46)N(2)O) production. Labeled nitrate ((15)NO(3)(-)) was immediately reduced to (30)N(2) in wet soil, whereas it was only reduced to (46)N(2)O in dry soil. Thus, the wet soil at the lower end of the catchment is a functional site for the scavenging for NO(3)(-) and N(2)O. Nitrite reductase gene (nirK and nirS) fragments from these soils were PCR amplified, cloned, and sequenced. Both nirK and nirS fragments were detected in the wet soil, whereas only nirK fragments were detected in the dry soil. All the nirK and nirS clones showed less than 90% similarity to known clones. Numerous operational taxonomic units for nirK and nirS were found in the wet soil. Considerable diversification within the largest clade on the nirK phylogenetic tree, which contained no known sequence, was observed in wet soil. Thus, a wet soil environment can provide both the habitat and conditions for the expression of denitrification activity.

An anaerobic continuous-flow fixed-bed reactor sustaining a 3-chlorobenzoate-degrading denitrifying population utilizing versatile electron donors and acceptors.

An anaerobic continuous-flow fixed-bed column reactor capable of degrading 3-chlorobenzoate (3-CBA) under denitrifying conditions was established, and its rate reached 2.26 mM d(-1). The denitrifying population completely degraded 3-CBA when supplied at 0.1-0.54 mM, but its activity was partly suppressed when 3-CBA was supplied at 0.89 mM. Nitrate was concomitantly consumed throughout the operation of the reactor, the amount of which was similar to or up to 35% higher than the theoretical stoichiometric value that was calculated by assuming that 3-CBA degradation is coupled with denitrification. Batch incubation experiments proved that nitrate is strictly required for 3-CBA degradation in the absence of molecular oxygen. The population also degraded 3-CBA aerobically. Benzoate and 4-CBA were degraded under denitrifying conditions as well as 3-CBA, but 2-CBA was not. Considering that the previously reported denitrifying 3-CBA-degrading cultures do not exhibit 4-CBA degradation under denitrifying conditions, nor aerobic 3-CBA degradation [FEMS Microbiol. Lett. 144 (1996) 213, Appl. Environ. Microbiol. 66 (2000) 3446], the microbial population developed in this experiment was physiologically versatile with respect to the utilization of both electron donors and electron acceptors.

Evidence for degradation of 2-chlorophenol by enrichment cultures under denitrifying conditions.

Although chlorophenol (CP) degradation has been studied, no bacterium responsible for degradation of CP under denitrifying conditions has been isolated. Moreover, little substantial evidence for anaerobic degradation of CPs coupled with denitrification is available even for mixed cultures. Degradation of CP [2-CP, 3-CP, 4-CP, 2,4-dichlorophenol (DCP) or 2,6-DCP] under denitrifying conditions was examined in anaerobic batch culture inoculated with activated sludge. Although 3-CP, 4-CP, 2,4-DCP and 2,6-DCP were not stably degraded, 2-CP was degraded and its degradation capability was sustained in a subculture. However, the rate of 2-CP degradation was not significantly enhanced by subculturing. In 2-CP-degrading cultures, nitrate was consumed stoichiometrically and concomitantly during 2-CP degradation, and a dechlorination intermediate was not detected, suggesting that 2-CP degradation was coupled with nitrate reduction. A 2-CP-degrading enrichment culture degraded 2-CP in the presence of nitrate, but did not in the absence of nitrate or the presence of sulfate. This suggests that the enrichment culture strictly requires nitrate for degradation of 2-CP. The apparent specific growth rate of the 2-CP degrading species was 0.0139 d(-1). Thus the apparent doubling time of the 2-CP-degrading population in the enrichment culture was greater than 50 d, which may explain difficulty in enrichment and isolation of micro-organisms responsible for CP degradation under denitrifying conditions.