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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]

The soluble fraction of ryegrass [Lolium perenne L. ssp. multiflorum (Lam.) Husnot.] straw comprises a major component of residue C and its presence or absence should influence the succession of decomposer communities. Changes in phospholipid fatty add (PLFA) profiles are indicative of shifts in microbial community structure. We used 13C-labeled ryegrass to track substrate-derived C into microbial lipids during decomposition in a microcosm-based study. Treatments were unleached straw, leached straw, and leachate, plus an unamended control. Destructive sampling took place after 0.6, 1.6, 15, 18, 50, and 80 d of incubation. Phospholipid fatty acids were extracted from bulk soil and isolated straw (detritusphere), and analyzed by gas chromatography combustion isotope ratio mass spectroscopy (GC-C-IRMS). Distinct temporal shifts occurred in PLFAs in bulk soil samples; cy19:0 was an indicator for late succession communities in unleached straw and leachate treatments, and 18:2ω6,9 characterized late samples in the leached straw treatment. The temporal shift was affected by the presence of the soluble fraction of straw. Microscale spatial effects were clear. Bulk soil and detritusphere communities were different and more 13C was detected in the 16:0 and 18:2ω6,9 PLFAs of the detritusphere than bulk soil. Carbon-13 was slowest to appear in PLFAs of leached straw samples, illustrating the importance of the soluble fraction in promoting growth of the biomass in bulk soil and in detritusphere. The 18:2ω6,9 PLFA, a fungal biomarker, was the most highly labeled in all treatments. Carbon-13 PLFA analysis provides greater insight into microbial community structure and functioning, facilitating more concrete conclusions regarding the role of functional groups of organisms. [ABSTRACT FROM AUTHOR]

The article reports on a study which examines the ability of Nitrobacter hamburgensis to metabolize lactate and explores its effect on lithoautotrophy. According the study, the response of N. hamburgensis to D- and L-lactate in the presence of mixotrophy and absence of organotrophy of NO- 2 was examined. The study shows that the L-lactate did not support organotrophic growth or stimulate mixotrophic growth. In contrast, D-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of NO- 2. The study suggests that lactate do not increase the rate of NO- 2 oxidation in N. hamburgensis, but instead lessens the NO- 2 requirement of the cell.

In mid latitude regions of North America, many soils are subjected to freeze-thaw conditions (Fr–Th) during the late winter and early spring months. Fr–Th events are usually accompanied by flushes of C and N mineralization, yet, the concomitant response of nitrification has not been consistently characterized. A laboratory experiment was conducted on three soils that differ in their annual history of exposure to freeze-thaw events, and where both ammonia oxidizing bacteria (AOB) and archaea (AOA) are capable of contributing to nitrification activity at 10 and 16 °C under NH 4 + replete conditions. Emergence and rates of N mineralization/nitrification were compared between soils frozen at −20 °C, with non-frozen soils stored at 4 °C. In all soils N mineralization commenced immediately (<1 d) in the Fr–Th soil treatments. Rates and/or amounts of mineralizable N released during the flush differed between soils, but rates for each soil were the same at 10 and 16 °C. Only ammonia oxidizing archaea (AOA)-driven nitrification emerged immediately (<1 d) from the Fr–Th treatment of the two soils with a history of freezing; these rates were higher at 16 than at 10 °C, and were not NH 4 + limited. No AOB activity was detected in these soils for up to 3 d. AOB contribute the vast majority (88–92%) of nitrification under NH 4 + replete conditions in the soil that rarely freezes. In this soil AOA did not contribute to nitrification in the Fr–Th treatment, and the emergence of AOB activity was delayed for 3 d at 10 °C unless supplemental NH 4 + was provided, but commenced immediately at 16 °C with or without supplemental NH 4 +; however, rates of nitrification at 10 and 16 °C did not differ. The dominance of AOA activity immediately after Fr–Th in soils with a history of freezing suggests that AOA handle the transition during the freeze-down phase, and/or recover during the freeze-thaw phase with less constraint of NH 4 + availability and temperature, than the AOB. • Nitrification was fully active in soils with a history of freezing within 1d of thawing. • Nitrification emerging from soil with a history of freezing was due to AOA activity. • Temperature of incubation affected the rate of AOA activity but not the emergence. • Nitrification emerging from soil with no history of freezing was due to AOB activity. • Temperature of incubation and NH 4 + availability influenced emergence of AOB activity. [ABSTRACT FROM AUTHOR]

The oxidation of ammonia (NH 3) to nitrite (NO 2 −) by archaea and bacteria (AOA and AOB) in soil has been studied intensively for >140 y. However, relatively little attention has been focused on the activity of nitrite oxidizing bacteria (NOB), which catalyze the oxidation of NO 2 −, despite ample published evidence of soil NO 2 − accumulation, and the temperature dependent accumulation of NO 2 − in wastewater and aquatic environments. This study evaluated the response of NO 2 − oxidizing activity to temperature in four Oregon agricultural soils. Rates of NO 2 − oxidizing potentials (NOP) were measured at 4–42 °C in all soils. Evaluation of the thermodynamic parameters found that the NOB have a similar temperature range and optimal temperature as the NH 3 oxidizer response observed in Taylor et al. (2016). A determination of kinetic parameters of NO 2 − oxidation at 17, 30, and 37 °C found a trend for the apparent maximum velocity (V max) to be greater at 30 than 17 °C, and significant, soil-specific changes in substrate affinity (K m) of NO 2 − consumption. Although the potential rates of NO 2 − oxidation exceeded those of NH 3 oxidation, NO 2 − accumulated under at least one temperature in all soils. There were only weak correlations between NO 2 − accumulation and rates of NH 3 or NO 2 − oxidation, the abundance of Nitrobacter nxr A or Nitrospira nxr B genes or the total (nxr A + nxr B)/ amo A gene ratio. The apparent K m did not correlate with NO 2 − accumulation at any temperature; however, utilizing the obtained V max and K m we found that Michaelis-Menten kinetics predict that an accumulation of measurable NO 2 − is required to drive equal rates of NH 3 and NO 2 − oxidation. Implications of reductions in NO 2 − affinity by NOB at some temperatures that result in increased NO 2 − accumulation in soils include plant toxicity and the loss of soil N through increased production of reactive N-oxide gases. Soil nitrite oxidizing bacteria (NOB) have similar temperature range and optimal temperature as the ammonia (NH 3) oxidizing archaea and bacteria (AOA and AOB). A determination of kinetic parameters of NO 2 − oxidation at 17, 30, and 37 °C found a trend for the apparent maximum velocity (V max) to be greater at 30 than 17 °C, and significant changes in substrate affinity (K m) of NO 2 − consumption. Utilizing the obtained V max and K m we found that Michaelis-Menten kinetics predict that an accumulation of measurable NO 2 − is required to drive equal rates of NH 3 and NO 2 − oxidation. Image 1 • NO 2 − oxidizing activity was measured at 4–42 °C in Oregon agricultural soils. • NH 3 and NO 2 − oxidizing bacteria share similar temperature ranges. • Substrate affinity (K m) of NO 2 − consumption changed in response to temperature. • NO 2 − accumulation is required to drive coupled nitrification at some temperatures. [ABSTRACT FROM AUTHOR]

The factors controlling the relative contributions of ammonia- (NH 3 ) oxidizing archaea (AOA) and bacteria (AOB) to nitrification and nitrous oxide (N 2 O) production in soil remain unclear. A study was conducted to examine the contributions of AOA and AOB to nitrification, nitrite (NO 2 − ) accumulation, and NO 2 − -affected N 2 O production in three non-cropped Oregon soils. Nitrification potential rates in the three soils ranged seven-fold from 0.15 to 1.08 μmol N g −1 d −1 , with AOA contributing 64–71% of the total activity. AOA- and AOB-driven NO 2 − accumulation represented 8–100% of total NO 2 − + NO 3 − accumulation, persisted over 48 h, and was accompanied by acetylene-sensitive, ammonium- (NH 4 + ) stimulated N 2 O production. Ammonium- and NO 2 − -dependent N 2 O production occurred when both AOA and AOB, or AOA alone were active. By adding the NO 2 − -oxidizing bacteria, Nitrobacter vulgaris , to soil slurries to increase NO 2 − -oxidizing capacity, both NO 2 − accumulation and N 2 O production were prevented, while the overall rate of nitrification was unaffected. Yields of N 2 O-N amounted to 0.05 ± 0.01% of total NO 2 − + NO 3 − -N accumulation in the presence of supplemental NH 4 + , and 0.28 ± 0.11% in the presence of both supplemental NH 4 + + NO 2 − . Regression analysis of the N 2 O production against NO 2 − accumulation over 24 h revealed a positive, non-linear relationship for N 2 O production by both AOA plus AOB and by AOA alone. Values of V max ranged 12-fold from 0.05 to 0.62 nmol N 2 O g −1 d −1 , and predicted K m values for NO 2 − ranged 15-fold from 0.02 to 0.30 μmol NO 2 − g −1 soil. These findings provide new insights into the impact of NO 2 − accumulation in soils on N 2 O production by both AOA and AOB, and show that NO 2 − accumulation primarily drives N 2 O formation in these soils, and increases N 2 O yield by both AOA and AOB. [ABSTRACT FROM AUTHOR]

The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH3) oxidation to nitrite (NO2-) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH3 oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH2OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH2OH or an initial oxidation product other than NH2OH. We now show through combined physiological and stable isotope tracer analyses that NH2OH is both produced and consumed during the oxidation of NH3 to NO2- by Nitrosopumilus maritimus, that consumption is coupled to energy conversion, and that NH2OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH3 by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH2OH, the archaea possibly catalyzing NH2OH oxidation using a novel enzyme complex. [ABSTRACT FROM AUTHOR]

Abstract: Dense hyphal mats formed by ectomycorrhizal (EcM) fungi are prominent features in Douglas-fir forest ecosystems, and have been estimated to cover up to 40% of the soil surface in some forest stands. Two morphotypes of EcM mats have been previously described: rhizomorphic mats, which have thick hyphal rhizomorphs and are found primarily in the organic horizon, and hydrophobic mats, which occur in the mineral horizon and have an ashy appearance. This study surveyed EcM mat and non-mat soils from eight early and late seral conifer forest stands at the H.J. Andrews Experimental Forest in western Oregon. EcM mats were classified by morphology and taxonomic identities were determined by DNA sequencing. A variety of chemical and biochemical properties, including enzymes involved in C, N, and P cycling were measured. Analysis was confined to a comparison of rhizomorphic mats colonizing the organic horizon with non-mat organic soils, and hydrophobic mats with non-mat mineral soils. Both the organic and mineral horizons showed differences between mat and non-mat enzyme profiles when compared on a dry weight basis. In the organic horizon, rhizomorphic mats had greater chitinase activity than non-mat soils; and in the mineral horizon, hydrophobic mats had increased chitinase, phosphatase, and phenoloxidase activity compared to the non-mat soil. The rhizomorphic mats had 2.7 times more oxalate than the non-mats and significantly lower pH. In the mineral horizon, hydrophobic mats had 40 times more oxalate and significantly lower pH than non-mat mineral soils. Microbial biomass C was not significantly different between the rhizomorphic mat and non-mat organic soils. In the mineral horizon, however, the hydrophobic mats had greater microbial biomass C than the non-mat soils. These data demonstrate that soils densely colonized by EcM fungi create a unique soil environment with distinct microbial activities when compared to non-mat forest soils. [Copyright &y& Elsevier]

The article explores the soluble butane monooxygenase's (sBMO) kinetic characterization from Thauera butanivorans. It notes that the three-component di-iron monooxygenase complex that is encoded by the C2-C9 alkane-utilizing bacterium T. butanivorans was depicted by evaluating substrate specificities for C1-C5 alkanes and product inhibition profiles. It adds that sBMO exhibits a high sequence homology with soluble methane monooxygenase (sMMO) and contributes a similar substrate range. It reveals that alkane oxidation by sBMO is differentiated for the consideration of C3-C5 alkanes and the ejection of various alcohol products.

Presents a study to determine effects of soil on the oxidation processes of halogenated and nonhalogenated hydrocarbons using Nitrosomonas europaea bacteria. Methodology used to conduct study; Indication of findings; Discussion on results.

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 (t 0.5  = 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.

Nitrosomonas europaea and Nitrobacter winogradskyi were grown singly and in co-culture in chemostats to probe for physiological differences between the two growth conditions. Co-culture growth medium containing 60 mM NH4 (+) resulted in a cell density (0.20-0.29 OD600) greater than the sum of the densities in single chemostat cultures, i.e., 0.09-0.14 OD600 for N. europaea with 60 mM NH4 (+)and 0.04-0.06 OD600 for N. winogradskyi with 60 mM NO2 (-). The NO2 (-)- and NH4 (+)-dependent O2 uptake rates, qRT-PCR, and microscopic observations indicated that in co-culture, N. europaea contributed ~0.20 OD600 (~80 %) and N. winogradskyi ~0.05 OD600 (~20 %). In co-culture, the transcriptomes showed that the mRNA levels of 773 genes in N. europaea (30.2 % of the genes) and of 372 genes in N. winogradskyi (11.8 % of the genes) changed significantly. Total cell growth and the analysis of the transcriptome revealed that in co-culture, N. europaea benefits more than N. winogradskyi.

Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed spacer region), eubacterial 16S rRNA, and archaeal 16S rRNA primers. Population size was measured with quantitative (Q)-PCR and composition was examined using length heterogeneity (LH)-PCR for fungal composition, terminal restriction fragment length (T-RFLP) profiles for bacterial and archaeal composition, and sequencing to identify dominant community members. Whereas fungal and archaeal composition varied between sites and dominant tree species, bacterial communities only varied between sites. The abundance of archaeal gene copy numbers was found to be greater in coastal compared to montane soils accounting for 11% of the prokaryotic community. Crenarchaea groups 1.1a-associated, 1.1b, 1.1c, and 1.1c-associated were putatively identified. A greater abundance of Crenarchaea 1.1b indicator fragments was found in acidic (pH 4) soils with low C:N ratios under red alder. In coastal soils, 25% of fungal sequences were putatively identified as basidiomycetous yeasts belonging to the genus Cryptococcus. Although the function of these yeasts in soil is not known, they could significantly contribute to decomposition processes in coastal soils distinguished by rapid tree growth, high N content, low pH, and frequent water-saturation events.

The placement of 'Pseudomonas butanovora' in the genus Thauera was proposed previously, based on 16S rRNA gene sequence analysis, upon further studies of taxonomical characteristics. In this study, physiological characteristics and DNA-DNA reassociation data are presented and the transfer of 'P. butanovora' to the genus Thauera is proposed. The original description of the strain (strain Bu-B1211) indicated that it was capable of denitrification but not anaerobic growth. 'P. butanovora' is capable of anaerobic respiration and growth, utilizing nitrate as a terminal electron acceptor during the oxidation of organic acids and alcohols, but not aromatic hydrocarbons or open-chain terpenoids. The total fatty acid composition supported the assignment of strain Bu-B1211 to the Betaproteobacteria and resembled that of members of the genus Thauera. The combination of 16S rRNA gene phylogenetic evidence, physiological and taxonomical characteristics and DNA-DNA reassociation data supported the placement of 'Pseudomonas butanovora' Bu-B1211 in the genus Thauera as representing a novel species, for which the name Thauera butanivorans sp. nov. is proposed. The type strain is Bu-B1211(T) (=IAM 12574(T)=ATCC 43655(T)=DSM 2080(T)).