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To reduce CH4 emissions, some dairy operations use manure as feedstock for anaerobic digesters, after which the nonvolatilized portion forms a digestate effluent with high NH4+ content that is used as fertilizer. When applied to soil, N fertilizers are subject to nitrification, where NH3–oxidizing archaea (AOA) and bacteria (AOB) oxidize NH3 to NO2–, NO2––oxidizing bacteria (NOB) oxidize NO2– to NO3−, and N oxides are produced from biotic and abiotic reactions. This study used soil microcosms to evaluate the properties of nitrification in response to the addition of N as digestate vs. NH4Cl in soils from the different climatic regions of the western Oregon coastal plain (CP) and eastern Oregon Columbia River basin (CRB). In each soil, properties of NH3 oxidation or N oxide accumulation did not differ when N was provided via digestate or NH4Cl over the normal temperature range; however, nitrification rates, communities, and products differed between soils. The average nitrification rate in CP soil was almost twofold higher than in CRB soil (P ≤.001), despite no significant differences in AOB activity or AOB amoA copy numbers. With N addition, AOA activity also increased in CP soil, where AOA amoA copy numbers were fivefold higher than CRB soil (P <.002). Accumulation of NO2– only in CRB soil was likely due to NOB inhibition by high NH3 concentrations (∼560 μM) present at the high pH of CRB soil (8.5). Overall, nitrification was dictated by differences in edaphic properties, temperature, and nitrifier communities more than N source. Core Ideas: Nitrification was not different between N sources at temperatures up to 30 °C.Ammonia‐oxidizing bacteria (AOB) activity did not differ between soils with high and low pH with N addition.Higher nitrification rates in low pH soil resulted from increased ammonia‐oxidizing archaea (AOA) activity.Lower AOA and NOB activity and abundances were found in high pH soil.High soil pH and low nitrifier abundances influenced NO2– and N oxide accumulation. [ABSTRACT FROM AUTHOR]

Abstract Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family. Results Of the three N. europaea fur homologs, only the Fur homolog encoded by gene NE0616 complemented the Escherichia coli H1780 fur mutant. A N. europaea fur:kanP mutant strain was created by insertion of kanamycin-resistance cassette in the promoter region of NE0616 fur homolog. The total cellular iron contents of the fur:kanP mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the fur:kanP mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the fur:kanP mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability. Conclusions Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by N. europaea NE0616 gene. Additional studies are required to fully delineate role of this fur homolog.

The factors influencing how soil nitrite (NO2-)- and ammonia (NH3)-oxidizing activities remain coupled are unknown. A short-term study (<48 h) was conducted to examine the dynamics of NO2--oxidizing activity and the accumulation of NO2- in three Oregon soils stimulated by the addition of 1 mM NH4+ in soil slurry. Nitrite initially accumulated in all three soils; its subsequent decline or slowing of the accumulation of the NO2- pool by 24 h was accompanied by an increase in the size of the nitrate (NO3-) pool, indicating a change in NO2- oxidation kinetics. Bacterial protein synthesis inhibitors prevented the NO2- pool decline, resulting in a larger accumulation in all three soils. Although no significant increases in NO2--oxidizing bacteria nxrA (Nitrobacter) and nxrB (Nitrospira) gene abundances were detected over the time course, maximum NO2- consumption rates increased 2-fold in the treatment without antibiotics compared to no change with antibiotics. No changes were observed in the apparent half saturation constant (Km) values for NO2- consumption. This study demonstrates phenotypic flexibility among soil NO2- oxidizers, which can undergo protein synthesis-dependent increases in NO2- consumption rates to match NH3 oxidation rates and recouple nitrification. [ABSTRACT FROM AUTHOR]

Ethene (ETH)-grown inocula of Nocardioides JS614 grow on vinyl chloride (VC), vinyl fluoride (VF), or vinyl bromide (VB) as the sole carbon and energy source, with faster growth rates and higher cell yields on VC and VF than on VB. However, whereas acetate-grown inocula of JS614 grow on VC and VF after a lag period, growth on VB did not occur unless supplemental ethene oxide (EtO) was present in the medium. Despite inferior growth on VB, the maximum rate of VB consumption by ETH-grown cells was ~ 50% greater than the rates of VC and VF consumption, but Br− release during VB consumption was non-stoichiometric with VB consumption (~ 66%) compared to 100% release of Cl− and F− during VC and VF consumption. Evidence was obtained for VB turnover-dependent toxicity of cell metabolism in JS614 with both acetate-dependent respiration and growth being significantly reduced by VB turnover, but no VC or VF turnover-dependent toxicity of growth was detected. Reduced growth rate and cell yield of JS614 on VB probably resulted from a combination of inefficient metabolic processing of the highly unstable VB epoxide (t0.5 = 45 s), accompanied by growth inhibitory effects of VB metabolites on acetate-dependent metabolism. The exact role(s) of EtO in promoting growth of alkene repressed JS614 on VB remains unresolved, with evidence of EtO inducing epoxide consuming activity prior to an increase in alkene oxidizing activity and supplementing reductant supply when VB is the growth substrate. [ABSTRACT FROM AUTHOR]

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP‡) was correlated with Topt across the eight soils, and the ΔCP‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments. [ABSTRACT FROM AUTHOR]

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. [ABSTRACT FROM AUTHOR]

Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-L-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-densityand growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS. [ABSTRACT FROM AUTHOR]

Although ammonia-oxidizing archaea (AOA ) and bacteria (AO B) coexist in most non-acidic agricultural soils, the factors that influence their relative contributions to soil nitrification activity remain unclear. A 2- to 4-d whole soil microcosm assay was developed, utilizing the aliphatic C8 alkyne 1-octyne to inactivate AO B-driven nitrification activity without impacting AOA nitrification activity. Responses of AOA - and AO B-supported net nitrification activities (accumulation of NO2- + NO3-) to different concentrations of extractable NH4 + were examined in four diverse, paired cropped and non-cropped Oregon soils sampled in summer and winter. Maximum AOA - supported net nitrification rates were significantly higher in non-cropped (3.7 mg N kg-1 soil d-1) than in cropped soils (0.9 mg N kg-1 soil d-1) and in summer (3.1 mg N kg-1 soil d-1) compared with winter soils (1.6 mg N kg-1 soil d-1). The NH4+ concentration required to significantly stimulate AOB nitrification activity was significantly higher in cropped soils (67 mg N kg-1 soil) than in non-cropped soils (12 mg N kg-1 soil). Maximum AO B activity was significantly higher in cropped (8.6 mg N kg-1 soil d-1) than in non-cropped soils (2.9 mg N kg-1 soil d-1) and in summer (7.8 mg N kg-1 soil d-1) compared with winter soils (3.8 mg N kg-1 soil d-1). This study revealed that AOA - and AO B-supported nitrification rates in cropped and non-cropped soils respond differently to season and NH4 + concentration and raises the possibility that AOA and AO B nitrification activities might be differentially managed to improve N use efficiency. [ABSTRACT FROM AUTHOR]

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH4+-availability that exist in the field. [ABSTRACT FROM AUTHOR]

Background: In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family. Results: Of the three N. europaea fur homologs, only the Fur homolog encoded by gene NE0616 complemented the Escherichia coli H1780 fur mutant. A N. europaea fur:kanP mutant strain was created by insertion of kanamycinresistance cassette in the promoter region of NE0616 fur homolog. The total cellular iron contents of the fur:kanP mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the fur:kanP mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the fur:kanP mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability. Conclusions: Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by N. europaea NE0616 gene. Additional studies are required to fully delineate role of this fur homolog. [ABSTRACT FROM AUTHOR]

A disturbance gradient was created to evaluate the relationship between changes in soil physical and chemical properties with microbial community composition. Plots of a 12-yr fallow Ultisol in Northeastern Brazil were arranged in a Latin Square design and disturbed by tillage events applied zero, one, two, three, or four times over a 3-mo period. Sixty days after the last event, plots were sampled (0-20 cm) and soil analyses performed. Tillage resulted in a linear disturbance gradient characterized by significant declines in soil available water, saturated hydraulic conductivity, soil aggregation, organic C, and microbial biomass. The disturbance gradient also affected soil microbial communities, but the changes observed were dependent on the profiling technique used. The application of one tillage event significantly altered terminal restriction fragment length polymorphism (T-RFLP) profiles, which remained unchanged on further disturbances. In contrast, community level physiological profiles (CLPPs) continued to change as disturbance levels increased and were significantly correlated with most soil properties associated with soil degradation. Phospholipid fatty acid (PLFA)-based assessment of microbial community structure was the least sensitive to disturbance, showing significant changes only between the control plots and those subjected to four tillage events. Nevertheless, the linear shift observed in a PLFA biomarker of bacterial stress (ratio of 1 9:0cy to 18:1 w7c) in response to the disturbance gradient was consistent with physiological changes in the CLPPs. The results clearly illustrate that microbial community responses to increasing levels of soil physical disturbance can be detected at physiological (CLPPs), biochemical (PLFA), and genotypic (T-RFLP) levels; however, they are not synchronously coupled. Further studies are needed to determine if there is functional significance to the physiological responses to disturbance that are, or are not, accompanied by consmunity composition changes. [ABSTRACT FROM AUTHOR]

Abstract: This study used inoculated, artificial soil microcosms containing sand, clay, cellulose, and localized “hotspots” of highly labile, organic N-containing dead bacteria to study N mineralization and assimilation at millimeter scales. Labeling with 15NH4 + along with measurement of its assimilation into microbial biomass at the bulk scale allowed estimation of gross rates of ammonification and N assimilation using isotope dilution. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) analyses of transects of organic-15N across Si wafers in contact with the microcosms indicated strong gradients of 15NH4 + assimilation as a function of proximity to the hotspots that were not apparent using bulk analyses. This combination of bulk and ToF-SIMS analyses represents a powerful approach to explore the physical and biochemical factors that affect N process heterogeneities in soils. [Copyright &y& Elsevier]

Abstract: Pseudomonas butanovora grows on butane by means of an inducible soluble alkane monooxygenase (sBMO). The induction of sBMO was studied using the wild type and a sBMO reporter strain. The reporter strain has the lacZ::kan cassette inserted into bmoX, the gene that encodes the α-subunit of the hydroxylase of sBMO. The β-galactosidase activity in the reporter strain was not induced by butane, but was induced by 1-butanol and butyraldehyde. P. butanovora expressed sBMO product-independent activity at 3.0±1nmolethylene oxidemin−1 mg protein−1 in stationary phase. The sBMO product-independent activity likely primes the expression of sBMO by butane. [Copyright &y& Elsevier]