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California has unsustainable use of agricultural water and energy, as well as problems of severe drought, nitrate pollution and groundwater salinity. As the leading producer and exporter of agricultural produce in the United States, 5.6 percent of California's energy is currently used for pumping groundwater. These problems and new regulatory policies (e.g., Sustainable Groundwater Management Act, Irrigated Lands Regulatory Program) pressure growers to schedule, account and maintain records of water, energy and nutrients needed for crop and soil management. Growers require varying levels of decision support to integrate different irrigation strategies into farm operations. Decision support can come from the public or private sector, where there are many tradeoffs between cost, underlying science, user friendliness and overall challenges in farm integration. Thus, effective irrigation management requires clear definitions, decision support and guidelines for how to incorporate and evaluate the water–nutrient–energy nexus benefits of different practices and combinations of practices under shifting water governance. The California Energy Commission-sponsored Energy Product Evaluation Hub (Cal-EPE Hub) project has a mission of providing science-based evaluation of energy-saving technologies as a direct result of improved water management for irrigation in agriculture, including current and future irrigation decision support systems in California. This project incorporates end-user perceptions into evaluations of existing decision support tools in partnership with government, agricultural and private stakeholders. In this article, we review the policy context and science underlying the available irrigation decision support systems (IDSS), discuss the benefits/tradeoffs and report on their efficacy and ease of use for the most prevalent cropping systems in California. Finally, we identify research and knowledge-to-action gaps for incorporating irrigation decision support systems into new incentives and requirements for reporting water and energy consumption as well as salinity and nitrogen management in the state of California. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Agriculture in California contributes 8% of the state's greenhouse gas (GHG) emissions. To inform the state's policy and program strategy to meet climate targets, we review recent research on practices that can reduce emissions, sequester carbon and provide other co-benefits to producers and the environment across agriculture and rangeland systems. Importantly, the research reviewed here was conducted in California and addresses practices in our specific agricultural, socioeconomic and biophysical environment. Farmland conversion and the dairy and intensive livestock sector are the largest contributors to GHG emissions and offer the greatest opportunities for avoided emissions. We also identify a range of other opportunities including soil and nutrient management, integrated and diversified farming systems, rangeland management, and biomassbased energy generation. Additional research to replicate and quantify the emissions reduction or carbon sequestration potential of these practices will strengthen the evidence base for California climate policy. [ABSTRACT FROM AUTHOR]

California's Mediterranean agro-ecosystems are a major source of U.S. fruits and vegetables, and vulnerable to future extremes of precipitation and temperature brought on by climate change, including increased drought and flooding, and more intense and longer heat waves. To develop resilience to these threats, strategies are necessary for climate-smart management of soil and water. Long-term, large-scale, replicated ecological experiments provide unique testbeds for studying such questions. At the UC Davis Russell Ranch Sustainable Agriculture Facility (RRSAF), the 100-year Century Experiment, initiated in 1992, is investigating the effects of multiple farming practices in a farm-scale replicated study of 10 row crop cropping systems. It includes different fertility management systems: organic, conventional and hybrid (conventional plus winter cover crop) systems; different crops: wheat, tomatoes, corn, alfalfa, cover crops and grasslands; and different irrigation systems: rainfed, flood irrigated and drip irrigated. We briefly describe and report on a selection of long-term experiments conducted at RRSAF investigating soil management and irrigation practices, which are an important focus for developing climate-smart strategies in Mediterranean systems. For example, long-term monitoring of soil carbon content revealed that most crop systems have experienced a small increase in soil carbon since 1993, and increases in organically managed plots were substantially higher. As RRSAF continues to build upon this rich dataset from one of a very few long-term row crop experiments in Mediterranean ecosystems, it provides a testbed for identifying climate-smart solutions for these agronomically important ecosystems. [ABSTRACT FROM AUTHOR]

A tracer plume was created within a thin aquifer by injection for 299 d of two adjacent 'sub-plumes' to represent one type of plume heterogeneity encountered in practice. The plume was monitored by snapshot sampling of transects of fully screened wells. The mass injection rate and total mass injected were known. Using all wells in each transect (0.77 m well spacing, 1.4 points/m2 sampling density), the Theissen Polygon Method (TPM) yielded apparently accurate mass discharge ( Md) estimates at three transects for 12 snapshots. When applied to hypothetical sparser transects using subsets of the wells with average spacing and sampling density from 1.55 to 5.39 m and 0.70 to 0.20 points/m2, respectively, the TPM accuracy depended on well spacing and location of the wells in the hypothesized transect with respect to the sub-plumes. Potential error was relatively low when the well spacing was less than the widths of the sub-plumes (>0.35 points/m2). Potential error increased for well spacing similar to or greater than the sub-plume widths, or when less than 1% of the plume area was sampled. For low density sampling of laterally heterogeneous plumes, small changes in groundwater flow direction can lead to wide fluctuations in Md estimates by the TPM. However, sampling conducted when flow is known or likely to be in a preferred direction can potentially allow more useful comparisons of Md over multiyear time frames, such as required for performance evaluation of natural attenuation or engineered remediation systems. [ABSTRACT FROM AUTHOR]

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. In the first experiment, a single recirculating well pair with bromide tracer and oxygen amendment successfully delivered oxygen to the subsurface for 42 d. 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 d 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Fluoroquinolones, a widely used class of antibiotics, are frequently detected in sediments and surface waters. Given their antimicrobial properties, the presence of these compounds may alter the composition of microbial communities and promote antibiotic resistance in the environment. The purpose of this study was to measure sorption, and effects of ciprofloxacin on microbial community composition, in sediment samples from three California salt marshes. Sediments were exposed to a ciprofloxacin concentration gradient (0–200 μg ml−1 ciprofloxacin) and microbial community composition characterized using phospholipid fatty acid (PLFA) analysis. Sorption coefficients, expressed as log Kd, were calculated from fits using the Freundlich isotherm model. Ciprofloxacin strongly sorbed to all sediments and had log Kd values, ranging from 2.9 to 4.3. Clay content was positively (r2=0.98) and pH negatively (r2=0.99) correlated to Kd values. Biomass, PLFA richness, sulfate reducer and Gram-negative bacteria markers increased with ciprofloxacin concentrations, while the 17 cy/precursor and saturated/unsaturated biomarker ratios, indicators of starvation stress, decreased. The magnitude of the effect of ciprofloxacin on microbial communities was inversely correlated to the degree of sorption to the sediments. Despite the fact that ciprofloxacin is a wide-spectrum antibiotic, its impact on sediment microbial communities was selective and appeared to favor sulfate-reducing bacteria and Gram-negative bacteria.The ISME Journal (2007) 1, 585–595; doi:10.1038/ismej.2007.71; published online 6 September 2007 [ABSTRACT FROM AUTHOR]

Phenanthrene mineralization rates were found to vary widely among four soils; differences in soil nutrient levels was one hypothesis to explain this variation. To test this hypothesis, phenanthrene mineralization rates were measured in these soils with, and without, added nitrogen and phosphorus. Mineralization rates either remained unchangedor were depressed by the addition of nitrogen and phosphorus. Phenanthrene degradation rates remained unchanged in the soil which had thehighest indigenous levels of nitrogen and phosphorus and which showed the largest increase in phosphorus levels after nutrients were added. The soils in which degradation rates were depressed had lower initial phosphorus concentrations and showed much smaller or no measurable increase in phosphorus levels after nutrients were added to the soils. To understand the response of phenanthrene degradation rates to added nitrogen and phosphorus, it may be necessary to consider the bioavailability of added nutrients and nutrient induced changes in microbial metabolism and ecology. [ABSTRACT FROM AUTHOR]

Abstract: The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4 =, NO3 −), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (>0.5 ng g−1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5–37 µg g−1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season. [Copyright &y& Elsevier]

Demonstrates methyl tert-butyl ether (MTBE) biodegradation supported by diffusive oxygen release with sediments from Vandenberg Air Force Base in Santa Barbara, California. Degradation of MTBE within the aerobic treatment zone; Decline in MTBE concentration in the active microcosms; Capability of microbial populations to degrade MTBE.

Investigates the use of bacterial strain PM1 in in situ bioremediation of methyl tertiary butyl ether (MTBE) groundwater contamination in Davis, California. Mineralization and degradation of MTBE; Application of the TaqMan quantitative polymerase chain reaction method to quantify bacteria; Result of the microcosm biodegradation.

• Compost amendments to tilled row crop increased SOM contents. • Long-term compost input enhanced macroaggregate formation. • Long-term compost input was associated with higher fungal populations. • Biochar addition had little impact on C dynamics and microbial communities. Soil organic amendments in agricultural production can benefit crop production and a wide range of soil properties, including soil aggregation. Soil aggregate formation is largely driven by microbial activities, and can in-turn influence microbial communities by generating distinct microbial habitats, as well as associated impacts on water and nutrient dynamics. We investigated the long-term effects of two fertilizer management strategies (poultry manure compost vs. mineral fertilizer) and biochar amendment (0 vs. 10 t ha−1 walnut shell biochar, 900 °C pyrolysis temperature, by-product of gasification) on soil aggregation, soil organic C, and microbial community dynamics in water-stable aggregate fractions in corn-tomato rotations. Using wet-sieving, soils (0–15 cm) were divided into four size fractions: large macroaggregates (2000–8000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay (<53 μm) for calculation of mean weight diameter in both 2014 and 2018. The total C and microbial community composition and abundance within each fraction were evaluated in 2018. Across all treatments, six years of continuous compost application maintained soil aggregate stability and C storage by increasing soil microbial biomass and associated dissolved organic C. Bacterial and fungal populations under compost treatments were significantly higher than under mineral fertilizer treatments based on 16S rRNA gene copy number and internal transcribed spacer (ITS) abundance, which likely contributed to the formation and maintenance of macroaggregates in compost treatments. Interestingly, continuous application of manure compost may increase microbial available C sources by increasing the abundance of bacteria with the potential to degrade aromatic C as predicted from 16S sequences. Soil under the mineral fertilizer treatment showed decreases in the proportion of large macroaggregates, bulk soil C, and aggregate-associated C storage compared to the compost treatment. The application of highly recalcitrant walnut shell biochar had limited long-term impacts on soil aggregation and C dynamics, likely due to its lack of microbially-available C and limited interaction with the soil environment. Our results indicate that continuous compost inputs maintained soil structure and associated physical stabilization of SOM by enlarging soil microbial available C pool, higher soil microbial biomass, and increasing aggregate formation. The soil aggregate structure, in-turn, generated diverse habitats and altered soil microbial communities. Compost inputs, in addition to or in partial replacement of mineral fertilizer inputs, can provide valuable microbial-driven ecosystem services, such as carbon storage and soil structure, while still providing fertility for crop growth. [ABSTRACT FROM AUTHOR]

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant- induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. [ABSTRACT FROM AUTHOR]

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.

A methyl tert-butyl ether (MTBE) / tert-butyl alcohol (TBA) plume originating from a gasoline spill in late 1994 at Vandenberg Air Force Base (VAFB) persisted for over 15 years within 200 feet of the original spill source. The plume persisted until 2010 despite excavation of the tanks and piping within months after the spill and excavations of additional contaminated sediments from the source area in 2007 and 2008. The probable history of MTBE concentrations along the plume centerline at its source was estimated using a wide variety of available information, including published details about the original spill, excavations and monitoring by VAFB consultants, and our own research data. Two-dimensional reactive transport simulations of MTBE along the plume centerline were conducted for a 20-year period following the spill. These analyses suggest that MTBE diffused from the thin anaerobic aquifer into the adjacent anaerobic silts and transformed to TBA in both aquifer and silt layers. The model reproduces the observation that after 2004 TBA was the dominant solute, diffusing back out of the silts into the aquifer and sustaining plume concentrations much longer than would have been the case in the absence of such diffusive exchange. Simulations also suggest that aerobic degradation of MTBE or TBA at the water table in the overlying silt layer significantly affected concentrations of MTBE and TBA by limiting the chemical mass available for back diffusion to the aquifer., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Side-by-side experiments were conducted in an aquifer contaminated with methyl-tert-butyl ether (MTBE) at a former fuel station to evaluate the effect of ethanol release on the fate of pre-existing MTBE contamination. On one side, for approximately 9 months we injected groundwater amended with 1-3 mg/L benzene, toluene, and o-xylene (BToX). On the other side, we injected the same, adding approximately 500 mg/L ethanol. The fates of BToX in both sides ("lanes") were addressed in a prior publication. No MTBE transformation was observed in the "No Ethanol Lane." In the "With Ethanol Lane", MTBE was transformed to tert-butyl alcohol (TBA) underthe methanogenic and/or acetogenic conditions induced by the in situ biodegradation of the ethanol downgradient of the injection wells. The lag time before onset of this transformation was less than 2 months and the pseudo-first-order reaction rate estimated after 7-8 months was 0.046 d(-1). Our results imply that rapid subsurface transformation of MTBE to TBA may be expected in situations where strongly anaerobic conditions are sustained and fluxes of requisite nutrients and electron donors allow development of an active acetogenic/methanogenic zone beyond the reach of inhibitory effects such as those caused by high concentrations of ethanol.

Methyl tert-butyl ether (MTBE) is a widespread groundwater contaminant that does not respond well to conventional treatment technologies. Growing evidence indicates that microbial communities indigenous to groundwater can degrade MTBE under aerobic and anaerobic conditions. Although pure cultures of microorganisms able to degrade or cometabolize MTBE have been reported, to date the specific organisms responsible for MTBE degradation in various field studies have not be identified. We report that DNA sequences almost identical (99% homology) to those of strain PM1, originally isolated from a biofilter in southern California, are naturally occurring in an MTBE-polluted aquifer in Vandenberg Air Force Base (VAFB), Lompoc, California. Cell densities of native PM1 (measured by TaqMan quantitative PCR) in VAFB groundwater samples ranged from below the detection limit (in anaerobic sites) to 10(3) to 10(4) cells/ml (in oxygen-amended sites). In groundwater from anaerobic or aerobic sites incubated in microcosms spiked with 10 microg of MTBE/liter, densities of native PM1 increased to approximately 10(5) cells/ml. Native PM1 densities also increased during incubation of VAFB sediments during MTBE degradation. In controlled field plots amended with oxygen, artificially increasing the MTBE concentration was followed by an increase in the in situ native PM1 cell density. This is the first reported relationship between in situ MTBE biodegradation and densities of MTBE-degrading bacteria by quantitative molecular methods.