The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest.

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities' response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi−bacteria (F:B) proportions between different trails (p = 2 × 10−16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism.

Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature.

Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.

Implications of the Thermodynamic Response of Soil Mineralization, Respiration, and Nitrification on Soil Organic Matter Retention.

Considerable research has shown that modifications in global temperature regimes can lead to changes in the interactions between soil respiration and the sequestration of C and N into soil organic matter (SOM). We hypothesized that despite the interconnected nature of respiration, net N mineralization, and nitrification processes, there would be differences in their thermodynamic responses that would affect the composition of inorganic soil N and the potential for retention of N in SOM. To test this hypothesis, soil respiration, N mineralization and nitrification responses were evaluated during constant temperature incubations at seven temperatures (4-42°C) in tilled and no-till soils from two major agroecological zones in Oregon; Willamette Valley, and Pendleton located in the Columbia River Basin. We observed (1) significant thermodynamic differences between the three processes in all soils, (2) a distinctly different thermodynamic profile in Willamette vs. Pendleton, and (3) a dynamic response of Topt (optimal temperature for activity), and Tsmax (temperature of greatest rate response to temperature), and temperature sensitivity (Δ C p ‡ ) over the incubation time course, resulting in shifts in the thermodynamic profiles that could not be adequately explained by changes in process rates. We found that differences in contributions of ammonia oxidizing archaea and bacteria to nitrification activity across temperature helped to explain the thermodynamic differences of this process between Willamette and Pendleton soils. A two-pool model of SOM utilization demonstrated that the dynamic thermodynamic response of respiration in the soils was due to shifts in utilization of labile and less-labile pools of C; and that the respiration response by Pendleton soils was more dependent upon contributions from the less-labile C pool resulting in higher Topt and Tsmax than Willamette soils. Interestingly, modeling of N mineralization using the two-pool model suggested that only the less-labile pool of SOM was contributing to N mineralization at most temperatures in all soils. The difference in labile and less-labile SOM pool utilization between respiration and N mineralization may suggest that these processes may not be as interconnected as previously thought.

Contrasting growth properties of Nocardioides JS614 on threedifferent vinyl halides.

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.

Nitrite-oxidizing activity responds to nitrite accumulation in soil.

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.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.

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.

Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria.

Ammonia (NH3)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH3 oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤ 20 µM concentrations of 1-alkynes C8 and C9. In contrast, NH3 oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 µM C8 (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH4(+)-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH4(+)-stimulated net nitrification rates of 2 and 7 µg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 µM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH4(+)-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.

A consideration of the relative contributions of different microbial subpopulations to the soil N cycle.

We examine and discuss literature targeted at identifying "active" subpopulations of soil microbial communities with regard to the factors that affect the balance between mineralization and immobilization/assimilation of N. Whereas a large fraction (≥50%) of soil microbial biomass can immediately respire exogenous substrates, it remains unclear what percentage of both bacterial and fungal populations are capable of expressing their growth potential. The factors controlling the relative amounts of respiratorily responsive biomass versus growth-active biomass will impact the balance between N mineralization and N immobilization. Stable isotope probing of de novo DNA synthesis, and pyrosequence analyses of rRNA:rDNA ratios in soils have identified both numerically dominant and rare microbial taxa showing greatest growth potential. The relative growth responses of numerically dominant or rare members of a soil community could influence the amount of N immobilized into biomass during a "growth" event. Recent studies have used selective antibiotics targeted at protein synthesis to measure the relative contributions of fungi and bacteria to ammonification and [Formula: see text] consumption, and of NH(3)-oxidizing archaea (AOA) and bacteria (AOB) to NH(3) oxidation. Evidence was obtained for bacteria to dominate [Formula: see text] assimilation and for fungi to be involved in both consumption of dissolved organic nitrogen (DON) and its ammonification. Soil conditions, phase of cropping system, [Formula: see text] availability, and soil pH influence the relative contributions of AOA and AOB to soil nitrification. A recent discovery that AOA can ammonify organic N sources and oxidize it to [Formula: see text] serves to illustrate roles for AOA in both the production and consumption of [Formula: see text]. Clearly, much remains to be learned about the factors influencing the relative contributions of bacteria, archaea, and fungi to processing organic and inorganic N, and their impact on the balance between mineralization and immobilization of N.

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

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 NH(4)(+)-availability that exist in the field.

Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses.

Ammonia-oxidizing bacteria and ammonia-oxidizing archaea are commonly found together in soils, yet the factors influencing their relative distribution and activity remain unclear. We examined archaeal and bacterial amoA gene distribution, and used a novel bioassay to assess archaeal and bacterial contributions to nitrification potentials in soils spanning a range of land uses (forest, pasture, cultivated and long-term fallowed cropland) along a 10 km transect. The assay, which quantifies the extent to which acetylene-inactivated soil nitrification potential recovers (RNP) in the presence of bacterial protein synthesis inhibitors, indicated a significant archaeal contribution to the nitrification potentials of the pasture and long-term fallowed soils. Archaeal amoA gene abundance did not vary significantly among the soils, but bacterial amoA gene abundance did, resulting in archaeal : bacterial amoA abundance ratios ranging from 1.1 ± 0.8 in cultivated soils to 396 ± 176 in pasture soils. Both archaeal and bacterial amoA gene compositions were heterogeneous across the landscape, but differed in their patterns of variability. Archaeal amoA gene distributions were distinct among each of the three main land-use types: forest, pasture and cropland soils. In contrast, bacterial amoA gene composition was distinct in forest and in cultivated cropland, while pasture and long-term fallowed cropland soils were similar. In both pasture and long-term fallowed cropland soils, one phylotype of Nitrosospira cluster 3a was highly abundant. This distinct bacterial amoA gene fingerprint correlated with significant contributions of archaea to RNP of both soils, despite differences in archaeal amoA gene composition between the pasture and fallowed soils. This observation suggests that the factors driving the development of ammonia-oxidizing bacteria community composition might influence the extent of archaeal contribution to soil nitrification.

Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils.

A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 µg/ml), whereas a combination of kanamycin plus gentamicin (800 µg/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30°C and 40°C and without supplemental NH(4)(+) (≤ 10 µM NH(4)(+) in solution), and pasture soil RNP demonstrated ∼ 50% insensitivity to 100 µM allyl thiourea (ATU). In addition, fallowed and pasture soil RNPs were insensitive to the fungal inhibitors nystatin and azoxystrobin. This combination of properties suggests that neither fungi nor AOB contributed to pasture soil RNP and that AOA were responsible for the RNP of the pasture soils. Both AOA and AOB may contribute to RNP in fallowed soil, while RNP in cropped soils was dominated by AOB.

Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide.

Nocardioides sp. strain JS614 grows on the C(2) alkenes ethene (Eth), vinyl chloride, and vinyl fluoride as sole carbon sources. The presence of 400-800 microM ethene oxide (EtO) extended the growth substrate range to propene (C(3)) and butene (C(4)). Propene-dependent growth of JS614 was CO(2) dependent and was prevented by the carboxylase/reductase inhibitor 2-bromoethanesulfonic acid, sodium salt (BES), while growth on Eth was not CO(2) dependent or BES sensitive. Although unable to promote growth, both propene and propene oxide (PrO)-induced expression of the genes encoding the alpha subunit of alkene monooxygenase (etnC) and epoxyethane CoM transferase (etnE) to similar levels as did Eth and EtO. Propene was transformed by Eth-grown and propene-grown/EtO-induced JS614 to PrO at a rate 4.2 times faster than PrO was consumed. As a result PrO accumulated in growth medium to 900 microM during EtO-induced growth on propene. PrO (50-100 microM) exerted inhibitory effects on growth of JS614 on both acetate and Eth, and on EtO-induced growth on Eth. However, higher EtO concentrations (300-400 microM) overcame the negative effects of PrO on Eth-dependent growth.

Utilization of fluoroethene as a surrogate for aerobic vinyl chloride transformation.

Fluoroethene (FE) is a stable molecule in aqueous solution and its aerobic transformation potentially yields F-. This work evaluated if FE is a suitable surrogate for monitoring aerobic vinyl chloride (VC) utilization or cometabolic transformation. Experiments were carried out with three isolates, Mycobacterium strain EE13a, Mycobacterium strain JS60, and Nocardioides strain JS614 to evaluate if their affinities for FE and VC and their rates of transformation were comparable and whether the transformation of FE and F- accumulation could be correlated with VC utilization. JS614 grew on FE in addition to VC, making it the first organism reported to use FE as a sole carbon and energy source. EE13a cometabolized VC and FE, and JS60 catabolized VC and cometabolized FE. There was little difference among the three strains in the Ks or kmax values for VC or FE. Competitive inhibition modeled the temporal responses of FE and VC transformations and Cl- and F- release when both substrates were present. Both the rate of FE transformation and rate of F-accumulation could be correlated with the rate of aerobic transformation of VC and showed promise for estimating VC rates in situ using FE as a reactive surrogate.

Relationships between patients' pre-treatment expectations of toxicities and post chemotherapy experiences.

A lack of adequate pharmacological explanations for side effect variation following chemotherapy suggests psychological factors may contribute to toxicity experience. This research aimed to determine if patients' expectations were associated with perceived toxicities for a wider range of chemotherapy toxicities than previously researched, including subjective and objective side effects. Eighty-seven chemotherapy-naive patients rated their expectations of 20 common side-effects before treatment, and then rated their experiences following their first chemotherapy dose. Hierarchical multiple regression analyses revealed that expectations of the inability to concentrate, hair loss, and diarrhoea prior to treatment had the strongest associations with the experience of symptoms. Expectations of encountering problems with sleep and sex, changes in taste or appetite, weakness, and nervousness, all showed moderate associations, and expectations of mood changes, feelings of tiredness, and nausea all showed weak associations with experience. These outcomes suggest that subjective side effects may be more prone to influence by expectation given their ambiguous nature. However, further research needs to be conducted into the effect expectations have on the treatment process, including the impact of other psychological factors. The current overriding emphasis placed on personal autonomy and fully informed consent may set up negative expectations which translate into adverse experiences to the detriment of the patient.