Impact of biochar on plant growth and uptake of ciprofloxacin, triclocarban and triclosan from biosolids.

Application of municipal biosolids in agriculture present a concern with potential uptake and bioaccumulation of pharmaceutical compounds from biosolids into agronomic plants. We evaluated the efficacy of biochar as a soil amendment to minimize uptake of antimicrobial agents (ciprofloxacin, triclocarban, and triclosan) in lettuce (Lactuca sativa) and carrot (Daucus carota) plants. Biochar reduced the concentration of ciprofloxacin and triclocarban in lettuce leaves and resulted in a 67% reduction of triclosan in carrot roots. There was no substantial difference in pharmaceutical concentrations in carrot and lettuce plant matter at low (2.0 g kg-1 soil) and high (20.4 g kg-1 soil) rates of applied biochar. The co-amendment of biochar and biosolids increased soil pH and nutrient content which were positively correlated with an increase in lettuce shoot biomass. Our results demonstrate the potential efficacy of using walnut shell biochar as a sorbent for pharmaceutical contaminants in soil without negatively affecting plant growth.

Deep soil inventories reveal that impacts of cover crops and compost on soil carbon sequestration differ in surface and subsurface soils.

Increasing soil organic carbon (SOC) via organic inputs is a key strategy for increasing long-term soil C storage and improving the climate change mitigation and adaptation potential of agricultural systems. A long-term trial in California's Mediterranean climate revealed impacts of management on SOC in maize-tomato and wheat-fallow cropping systems. SOC was measured at the initiation of the experiment and at year 19, at five depth increments down to 2 m, taking into account changes in bulk density. Across the entire 2 m profile, SOC in the wheat-fallow systems did not change with the addition of N fertilizer, winter cover crops (WCC), or irrigation alone and decreased by 5.6% with no inputs. There was some evidence of soil C gains at depth with both N fertilizer and irrigation, though high variation precluded detection of significant changes. In maize-tomato rotations, SOC increased by 12.6% (21.8 Mg C/ha) with both WCC and composted poultry manure inputs, across the 2 m profile. The addition of WCC to a conventionally managed system increased SOC stocks by 3.5% (1.44 Mg C/ha) in the 0-30 cm layer, but decreased by 10.8% (14.86 Mg C/ha) in the 30-200 cm layer, resulting in overall losses of 13.4 Mg C/ha. If we only measured soil C in the top 30 cm, we would have assumed an increase in total soil C increased with WCC alone, whereas in reality significant losses in SOC occurred when considering the 2 m soil profile. Ignoring the subsoil carbon dynamics in deeper layers of soil fails to recognize potential opportunities for soil C sequestration, and may lead to false conclusions about the impact of management practices on C sequestration.

The century experiment: the first twenty years of UC Davis' Mediterranean agroecological experiment.

The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of California, Davis provides long-term agroecological data from row crop systems in California's Central Valley starting in 1993. The Century Experiment was initially designed to study the effects of a gradient of water and nitrogen availability on soil properties and crop performance in ten different cropping systems to measure tradeoffs and synergies between agricultural productivity and sustainability. Currently systems include 11 different cropping systems-consisting of four different crops and a cover crop mixture-and one native grass system. This paper describes the long-term core data from the Century Experiment from 1993-2014, including crop yields and biomass, crop elemental contents, aerial-photo-based Normalized Difference Vegetation Index data, soil properties, weather, chemical constituents in irrigation water, winter weed populations, and operational data including fertilizer and pesticide application amounts and dates, planting dates, planting quantity and crop variety, and harvest dates. This data set represents the only known long-term set of data characterizing food production and sustainability in irrigated and rainfed Mediterranean annual cropping systems. There are no copyright restrictions associated with the use of this dataset.

Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1.

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.

Phenylurea herbicide sorption to biochars and agricultural soil.

Biochar is increasingly been used as a soil amendment to improve water-holding capacity, reduce nutrient leaching, increase soil pH, and also as a means to reduce contamination through sorption of heavy metals or organic pollutants. The sorption behavior of three phenylurea herbicides (monuron, diuron and linuron) on five biochars (Enhanced Biochar, Hog Waste, Turkey Litter, Walnut Shell and Wood Feedstock) and an agricultural soil (Yolo silt loam) was investigated using a batch equilibration method. Sorption isotherms of herbicides to biochars were well described by the Freundlich model (R(2) = 0.93-0.97). The adsorption KF values ranged from 6.94 to 1306.95 mg kg(-1) and indicated the sorption of herbicides in the biochars and Yolo soil was in the sequence of linuron > diuron > monuron and walnut shell biochar > wood feedstock biochar > turkey litter biochar > enhanced biochar > hog waste biochar > Yolo soil. These data show that sorption of herbicides to biochar can have both positive (reduced off-site transport) and negative (reduced herbicide efficacy) implications and specific biochar properties, such as H/C ratio and surface area, should be considered together with soil type, agriculture chemical and climate condition in biochar application to agricultural soil to optimize the system for both agricultural and environmental benefits.

Successful treatment of an MTBE-impacted aquifer using a bioreactor self-colonized by native aquifer bacteria.

A field-scale fixed bed bioreactor was used to successfully treat an MTBE-contaminated aquifer in North Hollywood, CA without requiring inoculation with introduced bacteria. Native bacteria from the MTBE-impacted aquifer rapidly colonized the bioreactor, entering the bioreactor in the contaminated groundwater pumped from the site, and biodegraded MTBE with greater than 99 % removal efficiency. DNA sequencing of the 16S rRNA gene identified MTBE-degrading bacteria Methylibium petroleiphilum in the bioreactor. Quantitative PCR showed M. petroleiphilum enriched by three orders of magnitude in the bioreactor above densities pre-existing in the groundwater. Because treatment was carried out by indigenous rather than introduced organisms, regulatory approval was obtained for implementation of a full-scale bioreactor to continue treatment of the aquifer. In addition, after confirmation of MTBE removal in the bioreactor to below maximum contaminant limit levels (MCL; MTBE = 5 µg L(-1)), treated water was approved for reinjection back into the aquifer rather than requiring discharge to a water treatment system. This is the first treatment system in California to be approved for reinjection of biologically treated effluent into a drinking water aquifer. This study demonstrated the potential for using native microbial communities already present in the aquifer as an inoculum for ex-situ bioreactors, circumventing the need to establish non-native, non-acclimated and potentially costly inoculants. Understanding and harnessing the metabolic potential of native organisms circumvents some of the issues associated with introducing non-native organisms into drinking water aquifers, and can provide a low-cost and efficient remediation technology that can streamline future bioremediation approval processes.

Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils.

The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.

Impacts of an ethanol-blended fuel release on groundwater and fate of produced methane: Simulation of field observations.

In a field experiment at Vandenberg Air Force Base (VAFB) designed to mimic the impact of a small-volume release of E10 (10% ethanol and 90% conventional gasoline), two plumes were created by injecting extracted groundwater spiked with benzene, toluene, and o-xylene, abbreviated BToX (No-Ethanol Lane) and BToX plus ethanol (With-Ethanol Lane) for 283 days. We developed a reactive transport model to understand processes controlling the fate of ethanol and BToX. The model was calibrated to the extensive field dataset and accounted for concentrations of sulfate, iron, acetate, and methane along with iron-reducing bacteria, sulfate-reducing bacteria, fermentative bacteria, and methanogenic archaea. The benzene plume was about 4.5 times longer in the With-Ethanol Lane than in the No-Ethanol Lane. Matching this different behavior in the two lanes required inhibiting benzene degradation in the presence of ethanol. Inclusion of iron reduction with negligible growth of iron-reducers was required to reproduce the observed constant degradation rate of benzene. Modeling suggested that vertical dispersion and diffusion of sulfate from an adjacent aquitard were important sources of sulfate in the aquifer. Matching of methane data required incorporating initial fermentation of ethanol to acetate, methane loss by outgassing, and methane oxidation coupled to sulfate and iron reduction. Simulation of microbial growth using dual Monod kinetics, and including inhibition by more favorable electron acceptors, generally resulted in reasonable yields for microbial growth of 0.01-0.05.

Effects of triclosan and biosolids on microbial community composition in an agricultural soil.

Triclosan (TCS) is a widely used antimicrobial agent found at high concentrations in biosolids produced during municipal wastewater treatment. The effect of adding TCS, in the presence or absence of biosolids, on the composition of an agricultural soil microbial community was measured using phospholipid fatty acid analysis (PLFA). Most changes observed in microbial community composition were attributable to the addition of biosolids or to the passage of time, with smaller changes due to TCS exposure, regardless of the presence of biosolids. TCS slightly reduced the relative abundance of Gram-positive and Gram-negative bacteria and fungi, with or without biosolids. Bacteria were more sensitive than eukaryotes, consistent with the mode of action of TCS, which selectively targets fatty acid synthesis and disrupts cell membranes of bacteria. TCS slightly increased biomarkers of microbial stress, but stress biomarkers were lower in all biosolid treated soils, presumably due to increased availability of nutrients mitigating potential TCS toxicity.

Effect of different transport observations on inverse modeling results: case study of a long-term groundwater tracer test monitored at high resolution.

Conservative tracer experiments can provide information useful for characterizing various subsurface transport properties. This study examines the effectiveness of three different types of transport observations for sensitivity analysis and parameter estimation of a three-dimensional site-specific groundwater flow and transport model: conservative tracer breakthrough curves (BTCs), first temporal moments of BTCs (m1), and tracer cumulative mass discharge (Md) through control planes combined with hydraulic head observations (h). High-resolution data obtained from a 410-day controlled field experiment at Vandenberg Air Force Base, California (USA), have been used. In this experiment, bromide was injected to create two adjacent plumes monitored at six different transects (perpendicular to groundwater flow) with a total of 162 monitoring wells. A total of 133 different observations of transient hydraulic head, 1,158 of BTC concentration, 23 of first moment, and 36 of mass discharge were used for sensitivity analysis and parameter estimation of nine flow and transport parameters. The importance of each group of transport observations in estimating these parameters was evaluated using sensitivity analysis, and five out of nine parameters were calibrated against these data. Results showed the advantages of using temporal moment of conservative tracer BTCs and mass discharge as observations for inverse modeling.

Using DNA-Stable Isotope Probing to Identify MTBE- and TBA-Degrading Microorganisms in Contaminated Groundwater.

Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with 13C5-MTBE, 13C1-MTBE (only methoxy carbon labeled), or13C4-TBA. 13C-DNA and 12C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading 13C-labeled MTBE and TBA in situ and the 13C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in the Burkholderiales and the Sphingomonadales orders were detected in all three13C clone libraries and were likely to be primary degraders at the site. Sequences related to sulfate-reducing bacteria and iron-reducers, such as Geobacter and Geothrix, were only detected in the clone libraries where MTBE and TBA were fully labeled with 13C, suggesting that they were involved in processing carbon from the tert-butyl group. Sequences similar to the Pseudomonas genus predominated in the clone library where only the methoxy carbon of MTBE was labeled with 13C. It is likely that members of this genus were secondary degraders cross-feeding on 13C-labeled metabolites such as acetate.

In Situ Biotreatment of TBA with Recirculation/Oxygenation.

The potential for in situ biodegradation of tert-butyl alcohol (TBA) by creation of aerobic conditions in the subsurface with recirculating well pairs was investigated in two field studies conducted at Vandenberg Air Force Base (VAFB). In the first experiment, a single recirculating well pair with bromide tracer and oxygen amendment successfully delivered oxygen to the subsurface for 42 days. TBA concentrations were reduced from approximately 500 µg/L to below the detection limit within the treatment zone and the treated water was detected in a monitoring transect several meters downgradient. In the second experiment, a site-calibrated model was used to design a double recirculating well pair with oxygen amendment, which successfully delivered oxygen to the subsurface for 291 days and also decreased TBA concentrations to below the detection limit. Methylibium petroleiphilum strain PM1, a known TBA-degrading bacterium, was detectable at the study site but addition of oxygen had little impact on the already low baseline population densities, suggesting that there was not enough carbon within the groundwater plume to support significant new growth in the PM1 population. Given favorable hydrogeologic and geochemical conditions, the use of recirculating well pairs to introduce dissolved oxygen into the subsurface is a viable method to stimulate in situ biodegradation of TBA or other aerobically-degradable aquifer contaminants.

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems.

This study coupled stable isotope probing with phospholipid fatty acid analysis ((13)C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced (13)C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 µm) and silt-and-clay (<53 µm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g(-1) soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g(-1) soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.

Land use and climatic factors structure regional patterns in soil microbial communities.

AIM: Although patterns are emerging for macroorganisms, we have limited understanding of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeographical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass. LOCATION: Great Basin Province, Desert Province and California Floristic Province, California, USA. METHODS: Using phospholipid fatty acid analysis, we compared microbial communities across eight land-use types sampled throughout the State of California, USA (n = 1117). RESULTS: The main factor driving composition and microbial biomass was land-use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here. MAIN CONCLUSIONS: Distinct microbial communities were associated with land-use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and management factors, such as flooding, tillage and irrigation, suggest that agricultural management can have larger effects on soil microbial communities than elevation and precipitation gradients.

Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments.

Real-time quantitative PCR assays, targeting part of the ammonia-monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with (15)N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 µm), microaggregate (53-250 µm), and silt-and-clay fraction (<53 µm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.- Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (~5.15×10(8) copies g(-1) soil). However, amoA gene densities were ~2 times higher in the organic (1.75×10(8) copies g(-1) soil) than the other systems at the start of the season and nosZ gene abundances were ~2 times greater in the conventional (7.65×10(7) copies g(-1) soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second hypothesis was also not corroborated because canonical correspondence analyses revealed that AOB and denitrifier abundances were decoupled from potential gross N mineralization and nitrification rates and from inorganic N concentrations. Our third hypothesis was supported by the overall larger nitrifier, denitrifier, and total bacterial communities measured in the soil microaggregates compared to the cPOM and silt-and-clay. These results suggest that the microaggregates are microenvironments that preferentially stabilize C, and concomitantly promote the growth of nitrifier and denitrifier communities, thereby serving as potential hotspots for N(2)O losses.

Quantitative gene monitoring of microbial tetracycline resistance using magnetic luminescent nanoparticles.

A magnetic/luminescent nanoparticles (MLNPs) based DNA hybridization method was developed for quantitative monitoring of antibiotic resistance genes and gene-expression in environmental samples. Manipulation of magnetic field enabled the separation of the MLNPs-DNA hybrids from the solution and the fluorescence of MLNPs normalized the quantity of target DNA. In our newly developed MLNPs-DNA assay, linear standard curves (R(2) = 0.99) of target gene was determined with the detection limit of 620 gene copies. The potential risk of increased bacterial antibiotic resistance was assessed by quantitative monitoring of tetracycline resistance (i.e., tetQ gene) in wastewater microcosms. The gene abundance and its expression showed a significant increase of tetQ gene copies with the addition of tetracycline, triclosan (TCS), or triclocarban (TCC). A real-time PCR assay was employed to verify the quantification capability of the MLNPs-DNA assay and accordingly both assays have shown strong correlation (R(2) = 0.93). This non-PCR based MLNPs-DNA assay has demonstrated its potential for gene quantification via a rapid, simple, and high throughput platform and its novel use of internal calibration standards.

[Effect of lignite humic acid on soil ammonia oxidizing archaea community].

OBJECTIVE: To illuminate the impact of humic acid (HA) on soil ammonia oxidizing archaea and then reveal the effect of HA on soil nitrogen cycle. METHODS: Two humic acids (cHA and bHA) were added into the soil amended with urea. Community changes of ammonia oxidizing archaea (AOA) and total archaea were studied with terminal restricted fragment length polymorphism (T-RFLP) and real time PCR in the microcosm experiment. RESULTS: We found that the AOA population size increased significantly and AOA community changed greatly in the urea only treatment. However, HA could inhibit the increase of AOA population, moreover, HA could buffer the change in AOA community showed by canonical correspondence analysis (CCA) result. On the other hand, the total archaeal population decreased significantly in the urea only treatment, but stabilized in the urea with HA treatments, which indicated HA could eliminate the toxicity of urea to total archaea. CCA results showed that incubation time was the most important factor for the total archaeal community, and partial CCA (pCCA, when time as a covariable) result demonstrated that cHA was the most important environmental variable for total archaeal community. CONCLUSION: These results showed that HA diminished ammonia loss by inhibiting the increase of AOA competing with plant for ammonia, thus HA can increase the urea efficiency.

Impact of Irrigation Strategies on Tomato Root Distribution and Rhizosphere Processes in an Organic System.

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

Humic acids buffer the effects of urea on soil ammonia oxidizers and potential nitrification.

Humic acids (HAs) play an important role in the global nitrogen cycle by influencing the distribution, bioavailability, and ultimate fate of organic nitrogen. Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in ecosystems and is limited, in part, by the availability of [Formula: see text]. We evaluated the impact of HAs on soil AOB in microcosms by applying urea (1.0%, equal to 10 mg urea/g soil) with 0.1% bHA (biodegraded lignite humic acids, equal to 1 mg/g soil), 0.1% cHA (crude lignite humic acids) or no amendment. AOB population size, ammonium and nitrate concentrations were monitored for 12 weeks after urea and HA application. AOB densities (quantified by real-time PCR targeting the amoA) in the Urea treatments increased about ten-fold (the final abundance: 5.02 × 10(7) copies (g of dry soil)(-1)) after one week of incubation and decreased to the initial density after 12 weeks incubation; the population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) decreased from 1.12 × 10(10) to 2.59 × 10(9) copies (g of dry soil)(-1) at week one and fluctuated back to the initial copy number at week 12. In the Urea + bHA and Urea + cHA treatments, the AOB densities were 4 and 6 times higher, respectively, than the initial density of approximately 5.07 × 10(6) copies (g of dry soil)(-1) at week 1 and did not change much up to week 4; the total bacteria density changed little over time. The AOB and total bacteria density of the controls changed little during the 12 weeks of incubation. The microbial community composition of the Urea treatment, based on T-RFLP using CCA (canonical correspondence analysis) and pCCA (partial CCA) analysis, was clearly different from those of other treatments, and suggested that lignite HAs buffered the change in diversity and quantity of total bacteria caused by the application of urea to the soil. We hypothesize that HAs can inhibit the change in microbial community composition and numbers, as well as AOB population size by reducing the hydrolysis rate from urea to ammonium in soils amended with urea.