Bacteria from hydrocarbon seep areas growing on short-chain alkanes

Marine hydrocarbon seeps introduce large amounts of organic carbon into the environment. Different microorganisms inhabit these unusual environments using the hydrocarbons as an energy source. A recent paper by Kniemeyer et al. shows, for the first time, that sulfate-reducing bacteria isolated from hydrocarbon seeps can oxidize short-chain hydrocarbons anaerobically. This finding is an important contribution to our understanding of the role of microbes in the recycling of chemically inactive carbon compounds.     

Soil ingestion estimates for use in site evaluations based on the best tracer method

This paper develops a novel methodology, the Best Tracer method (BTM), that substantially overcomes the principal limitations (intertracer inconsistencies, and poor precision of recovery) of estimating soil ingestion by specific soil‐based tracers in massbalance studies. The BTM incorporates a biological and statistical framework that improves precision of recovery of tracer estimates, markedly reducing input‐output misalignment error resulting from a lack of correspondence between food tracer input and fecal tracer output.

This method is then used to re‐estimate the soil ingestion distribution of previously published soil ingestion estimates from two children studies (Calabrese et al. 1989; Davis et al., 1990) and one adult study (Calabrese et al., 1990). Revised estimates of soil ingestion are provided for each study. In addition, the results from the two children's studies are combined to form a single estimate of the soil ingestion distribution. These collective findings result in more reliable quantitative estimates of soil ingestion than trace element specific estimates, as well as providing improved understanding of current published soil ingestion studies, and improved methods that will enhance the design and interpretation of future soil ingestion studies.

With respect to children, the data indicate that the Calabrese et al. (1989) study provides the most reliable estimates of soil ingestion based on the estimated precision of recovery. However, estimates for the combined data of the Calabrese et al. (1989) and Davis et al. (1990) studies include all available children's data from mass balance studies, and thus provide more robust estimates. The collective data suggest that the median child in these studies ingested 30–40 mg/day of soil, while the upper 95% estimate is approximately 200 mg/day. Current data are insufficient to distinguish the children's soil ingestion distribution from that of adults. The revised and improved estimates of soil ingestion for children and adults have important implications for contaminant exposure estimates used in site evaluation risk assessment procedures.     

Petroleum bioremediation — a multiphase problem

Microbial degradation of hydrocarbons is a multiphase reaction, involving oxygen gas, water-insoluble hydrocarbons, water, dissolved salts and microorganisms. The fact that the first step in hydrocarbon catabolism involves a membrane-bound oxygenase makes it essential for microorganisms to come into direct contact with the hydrocarbon substrate. Growth then proceeds on the hydrocarbon/water interface. Bacteria have developed two general strategies for enhancing contact with water-insoluble hydrocarbons: specific adhesion mechanisms and production of extracellular emulsifying agents. Since petroleum is a complex mixture of many different classes of hydrocarbons, of which any particular microorganism has the potential to degrade only part, it follows that the microorganisms must also have a mechanism for desorbing from used' oil droplets.The major limitations in bioremediation of hydrocarbon-contaminated water and soil is available sources of nitrogen and phosphorus. The usual sources of these materials, e.g. ammonium sulfate and phosphate salts, have a high water solubility which reduces their effectiveness in open systems because of rapid dilution. We have attempted to overcome this problem by the use of a new controlled-release, hydrophobic fertilizer, F-1, which is a modified urea-formaldehyde polymer containing 18% N and 10% P as P₂O₅. Microorganisms were obtained by enrichment culture that could grow on crude oil as the carbon and energy source and F-1 as the nitrogen and phosphorus source. The microorganisms and the F-1 adhered to the oil/water interface, as observed microscopically and by the fact that degradation proceeded even when the water phase was removed and replaced seven times with unsupplemented water — a simulated open system. Strains which can use F-1 contain a cell-bound, inducible enzyme which depolymerizes F-1.After optimizing conditions in the laboratory for the use of F-1 and the selected bacteria for degrading crude oil, a field trial was performed on an oil contaminated sandy beach between Haifa and Acre, Israel, in the summer of 1992. The sand was treated with 5 g F-1 per kg sand and inoculated with the selected bacteria; the plot was watered with sea water and plowed daily. After 28 days the average hydrocarbon content of the sand decreased from 5.1 mg per g sand to 0.6 mg per g sand. Overall, there was an approx. 86% degradation of pentane extractables as demonstrated by dry weight, I.R. and GLC analyses. An untreated control plot showed only a 15% decrease in hydrocarbons. During the winter of 1992, the entire beach (approx. 200 tons of crude oil) was cleaned using the F-1 bacteria technology. The rate of degradation was 0.06 mg g^-1 sand day^-1 (10°C) compared to 0.13 mg g^-1 sand day^-1 during the summer (25°C).     

Biodegradation of Aliphatic vs. Aromatic Hydrocarbons in Fertilized Arctic Soils

The objectives of this study were to (1) test a simple bioremediation treatment strategy in the Arctic and (2) examine the effect of fertilization on the degradation of aliphatic and aromatic hydrocarbons. The site is a coarse sand pad that once supported fuel storage tanks. Concentrations of diesel-range organics at the beginning of the study (July 1996) ranged from 250 to 860 mg/kg soil. Replicate field plots treated with fertilizer yielded final concentrations of 0, 50, 100, or 200 mg N/kg soil. Soil samples were collected three times during the thaw season and analyzed for physical and chemical properties, microbial populations and activities, and concentrations of semivolatile hydrocarbons. Soil pH and soil-water potentials declined as a result of fertilizer application. Addition of fertilizer significantly increased soil respiration potentials, but not the populations of microorganisms measured. Fertilizer addition also resulted in ∼50% loss of measured aliphatic and aromatic hydrocarbons in surface and subsurface soils. For fertilized plots, hydrocarbon loss was not related to the amount of fertilizer added. Losses of aliphatic hydrocarbons were attributed to biotic processes, whereas losses of aromatic hydrocarbons likely were a result of both biotic and abiotic processes.     

Hydrocarbon Leaching, Microbial Population, and Plant Growth in Soil Amended with Petroleum

Two samples of oily waste organics (OWO) from petroleum wells were added to heath soils from Tierra del Fuego, Argentina, and the effects on hydrocarbon leaching, microbial population, and plant growth were studied. These mixtures and a control soil were subjected to four deionized water leachates. For each leachate, total petroleum hydrocarbons (TPH), aliphatic hydrocarbons (ALH), aromatic hydrocarbons (ARH) with three or fewer rings, ARH with more than three rings, and oil and grease (O&G) were measured. After leaching, six Dactylis glomerata L. plants were grown in each soil column. Plant growth and the total number of aerobic and nitrifier microorganisms were measured in soil. The 10% OWO sample increased the TPH in the leachate, but the 1% sample did not. The ALH, ARH, and O&G of each leachate followed patterns similar to that for TPH. Plant growth diminished and the total number of aerobic and nitrifier microorganisms decreased with increasing OWO, especially when the OWO was from a fresh residue rather than an aged residue. The greater inhibitive effect of fresh residue on plant growth was attributed to a higher concentration of light hydrocarbons, which are more toxic than heavy hydrocarbons. For soil with 1% OWO added, the TPH and other organics did not differ from the control soil. This result, combined with the 10-year average annual rainfall and the water table elevation at the site, suggests that the risk of contaminating the water table is relatively low. Thus, a 1% addition of OWO in soil would be appropriate to use in landfarming of OWO.     

Bacterial Community Dynamics during Bioremediation of Diesel Oil-Contaminated Antarctic Soil

The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated using biostimulation with nutrients, and that this causes a change in the indigenous bacterial communities and in the genetic potential for hydrocarbon degradation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enhancement of Hydrocarbon Removal in a Clay and Drilling-Waste Polluted Soil

The application of biological processes in restoring oil polluted sites is growing due to their efficiency in removing different classes of pollutants. The aim of this study was to determine the ability of microorganisms present in a drilling-waste polluted soil (36,200 mg TPH kg^?1 soil) to remove weathered hydrocarbons under stimulated and non-stimulated soil conditions. The hypothesis under study was whether petroleum hydrocarbons removal could be enhanced by manipulating C/N ratio, water content and addition of three agroindustrial wastes. A Box-Behnken design was employed to evaluate the effect of each variable. Results demonstrated that, for orange peels and banana trunk treatments, the variable with the largest effect (p < 0.01) on hydrocarbon removal was the C/N ratio, indicating that higher ratio (100/3) improved removal (79.5–82%). The largest effect (p < 0.001) on hydrocarbon removal for pineapple wastes was observed with higher water content (60%) achieving the highest removal (89%). After 90 days of experimentation, the type of agricultural waste and the agricultural waste/soil ratio were not statistically significant in any treatment. However, their addition was important relative to non-stimulated soil, which showed a hydrocarbon removal of 17%. Data reported in this study showed the application of bioremediation in clay and drilling waste-polluted soils.     

Influence of climate variability on plant production and N‐mineralization in Central US grasslands

Abstract. We assessed the influence of annual and seasonal climate variability over soil organic matter (SOM), above‐ground net primary production (ANPP) and in situ net nitrogen (N) mineralization in a regional field study across the International Geosphere Biosphere Programme (IGBP) North American mid‐latitude transect (Koch et al. 1995). We hypothesized that while trends in SOM are strongly correlated with mean climatic parameters, ANPP and net N‐mineralization are more strongly influenced by annual and seasonal climate because they are dynamic processes sensitive to short‐term variation in temperature and water availability. Seasonal and monthly deviations from long‐term climatic means, particularly precipitation, were greatest at the semi‐arid end of the transect. ANPP is sensitive to this climatic variability, but is also strongly correlated with mean annual climate parameters. In situ net N‐mineralization and nitrification were weakly influenced by soil water content and temperature during the incubation and were less sensitive to seasonal climatic variables than ANPP, probably because microbial transformations of N in the soil are mediated over even finer temporal scales. We found no relationship between ANPP and in situ net N‐mineralization. These results suggests that methods used to estimate in situ net N‐mineralization are inadequate to represent N‐availability across gradients where microbial biomass, N‐immobilization or competition among plants and microbes vary.     

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG‐RAST, Actinomycetales (9.8%) were found to be the dominant microorganisms, followed by Rhizobiales (3.3%). Furthermore, several functional genes were found in this study, mostly belong to Actinobacteria (12.35%), which have a role in the metabolism of aliphatic and aromatic hydrocarbons (2.51%), desulfurization (0.03%), element shortage (5.6%), and resistance to heavy metals (1.1%). This information will be useful for assisting in the application of microorganisms in the removal of hydrocarbon contamination and/or for improving the quality of crude oil. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:638–648, 2016     

Biodegradation and bioremediation of hydrocarbons in extreme environments

Many hydrocarbon-contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, high salt concentrations, or high pressure, Hydrocarbon-degrading microorganisms, adapted to grow and thrive in these environments, play an important role in the biological treatment of polluted extreme habitats. The biodegradation (transformation or mineralization) of a wide range of hydrocarbons, including aliphatic, aromatic, halogenated and nitrated compounds, has been shown to occur in various extreme habitats. The biodegradation of many components of petroleum hydrocarbons has been reported in a variety of terrestrial and marine cold ecosystems. Cold-adapted hydrocarbon degraders are also useful for wastewater treatment. The use of thermophiles for biodegradation of hydrocarbons with low water solubility is of interest, as solubility and thus bioavailability, are enhanced at elevated temperatures. Thermophiles, predominantly bacilli, possess a substantial potential for the degradation of environmental pollutants, including all major classes. Indigenous thermophilic hydrocarbon degraders are of special significance for the bioremediation of oil-polluted desert soil. Some studies have investigated composting as a bioremediation process. Hydrocarbon biodegradation in the presence of high salt concentrations is of interest for the bioremediation of oil-polluted salt marshes and industrial wastewaters, contaminated with aromatic hydrocarbons or with chlorinated hydrocarbons. Our knowledge of the biodegradation potential of acidophilic, alkaliphilic, or barophilic microorganisms is limited.     

Microbial degradation of model petroleum at low temperatures

Two areas of Chesapeake Bay, Colgate Creek in Baltimore Harbor and Eastern Bay, are presently under study, with routine sampling of water and sediment for petroleum-degrading microorganisms (bacteria, yeasts, and fungi) by direct plating and enrichment culture. Selected physical and chemical parameters are recorded for each sampling site, and water and sediment samples are extracted for hydrocarbons. Numbers of petroleum-degrading microorganisms enumerated by direct plating were found to correlate with the concentration of benzene-extractable material and were higher for the Colgate Creek than for the Eastern Bay site. Petroleum-degrading microorganisms were isolated from water and sediment samples at environmental temperatures of 0°, 5°, and 10°C. A salts medium supplemented with nitrate and phosphate was used to provide optimum conditions for petroleum degradation, whereas Chesapeake Bay water was used to simulate natural environmental conditions. Use of a model petroleum permitted quantitative measurement of utilization of individual hydrocarbons ranging in complexity from simple alkanes to polynuclear aromatic hydrocarbons. Higher growth yields and maximum hydrocarbon degradation was observed for microorganisms in the salts medium at 0°, 5°, and 10°C, although significant quantities of hydrocarbons were utilized in some samples grown in a medium for which Chesapeake Bay water was the diluent. Bacterial hydrocarbon degradation accounted for most of the model petroleum utilization at 0° and 5°C. However, oscillations of bacterial populations, with significant growth of yeasts, was observed at 10°C. Photomicroscopy and scanning electron microscopy revealed aggregates of bacteria, yeasts, and fungi associated with oil globules. From preliminary identification and classification of the hydrocarbon-utilizing bacteria, members of the generaVibrio, Aeromonas, Pseudomonas, andAcinetobacter were present in the enrichment cultures. From results of this study, it is concluded that utilization of model petroleum at low temperatures is a function of the types and numbers of microorganisms present in an original inoculum taken from the natural environment.     

CFTR: Domains, Structure, and Function

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis (CF) (Collins, 1992). Over 500 naturally occurring mutations have been identified in CF gene which are located in all of the domains of the protein (Kerem et al., 1990; Mercier et al., 1993; Ghanem et al., 1994; Fanen et al., 1992; Ferec et al., 1992; Cutting et al., 1990). Early studies by several investigators characterized CFTR as a chloride channel (Anderson et al.; 1991b,c; Bear et al., 1991). The complex secondary structure of the protein suggested that CFTR might possess other functions in addition to being a chloride channel. Studies have established that the CFTR functions not only as a chloride channel but is indeed a regulator of sodium channels (Stutts et al., 1995), outwardly rectifying chloride channels (ORCC) (Gray et al., 1989; Garber et al., 1992; Egan et al., 1992; Hwang et al., 1989; Schwiebert et al., 1995) and also the transport of ATP (Schwiebert et al., 1995; Reisin et al., 1994). This mini-review deals with the studies which elucidate the functions of the various domains of CFTR, namely the transmembrane domains, TMD1 and TMD2, the two cytoplasmic nucleotide binding domains, NBD1 and NBD2, and the regulatory, R, domain.     

187 Plucking the high hanging fruit: a systematic approach for targeting protein interfaces

Development of specific ligands for protein targets that help decode the complexities of protein–protein interaction networks is a key goal for the field of chemical biology. Despite the emergence of powerful in silico and experimental high-throughput screening strategies, the discovery of synthetic ligands that selectively modulate protein–protein interactions remains a challenge for the chemical biologists. Proteins often utilize small folded domains for recognition of other biomolecules. The basic hypothesis guiding our research is that by mimicking these domains, we can modulate the function of a particular protein with metabolically-stable synthetic molecules (Raj et al., 2013). This presentation will discuss computational approaches (Bullock et al., 2011; Jochim & Arora, 2010) to identify targetable interfaces along with synthetic methods (Patgiri et al., 2008; Tosovska & Arora, 2010) to develop protein domain mimics (PDMs) as modulators of intracellular protein–protein interactions (Henchey et al., 2010; Patgiri et al., 2011).     

A Guide to Interpreting Soil Ingestion Studies. 2. Qualitative and Quantitative Evidence of Soil Ingestion

Abstract

Four major studies have attempted to qualitatively and quantitatively assess the extent of soil ingestion in children using the soil tracer methodology. The validity of the estimates of soil ingestion of each study was reevaluated in light of the inherent strengths and limitations of study design and/or execution as well as via a novel methodology to estimate the soil recovery variance of each tracer which then lead to the estimation of soil ingestion detection limits of each tracer for studies performing mass-balance analyses. Based on these analyses it is concluded that the Binder et al. (1986) and Van Wijnen et al. (1990) studies provide no convincing evidence to support qualitative and quantitative estimates of soil ingestion due to inherent limitations of their respective study designs. The Davis et al. (1990) and Calabrese et al. (1989) studies displayed convincing qualitative evidence of soil ingestion. However, the results indicate that the median soil ingestion estimates of Davis et al. were less reliable than those of Calabrese et al. The range of detection limits vary according to the tracer and the assumption of acceptable precision in recovery estimation. The minimum detection level of soil ingestion in children in the Calabrese et al. study with a variance in recovery of 100% ± 20% was 16 mg day^?1 based on Zr.

These findings are of particular regulatory significance since they provide: (1) a method of assessing the level of detection inherent in soil ingestion studies, (2) a reevaluation of the major soil ingestion studies in light of new methodology, and (3) guidance for future studies so that detection capacity can now be included in the presentation of study findings.     

Investigation of Microbes in the Rhizosphere of Selected Trees for the Rhizoremediation of Hydrocarbon-Contaminated Soils

Hydrocarbon-degrading microorganisms (HDMs), associated with the rhizosphere of Conocarpus lancifolius and Ficus infectoria trees grown in bioremediated soil, were isolated under controlled laboratory conditions. The selected trees were used to phytoremediate oil-contaminated soil for three successive growing seasons. At the end of the phytoremediation experiment, 85.7% of measurable total petroleum hydrocarbon was degraded in the rhizosphere soil associated with Conocarpus lancifolius compared to 78.6% in the rhizosphere of Ficus infectoria. The detectable concentrations of some polyaromatic hydrocarbons were less than 0.02 ppm. The HDM isolation process was conducted at 35°C under aerobic conditions. The isolated HDMs were identified using 16S rRNA gene sequencing and fatty acid methyl ester analysis. Differences in the genera of the isolated HDMs and their assessed efficiency in degrading a mixture of hydrocarbon compounds between the two trees were noted.     

Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass

Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses to drought. Critically, a drought experiment utilizing small pots in the greenhouse elicited nearly identical physiological changes as an experiment conducted in the field, but an order of magnitude more differentially expressed genes. However, we were able to define a suite of several hundred genes that were differentially expressed across all experiments. This list was strongly enriched in photosynthesis, water status, and reactive oxygen species responsive genes. The strong across-experiment correlations between physiological plasticity—but not differential gene expression—highlight the complex and diverse genetic mechanisms that can produce phenotypically similar responses to various soil water deficits.Crop productivity and wild plant distributions are governed by the availability of soil moisture (Axelrod, 1972; Boyer, 1982; Ciais et al., 2005). The impact of drought and soil water deficit in agriculture is estimated to be the largest abiotic determinant of yield (Boyer, 1982; Araus et al., 2002), while drought is also considered a primary cause of speciation and adaptation in nature (Stebbins, 1952). Dehydration avoidance and other drought adaptive strategies permit plants to survive or maintain growth during periodic droughts (Blum, 1996; Chaves et al., 2003; Chaves and Oliveira, 2004). Specifically, phenotypic plasticity of stomatal conductance, water foraging, and growth traits (among many others) may effectively maintain homeostasis of leaf water potential despite soil water deficits.Leaf water potential is a bellwether of the physiological impact of water deficit (Jones, 2007). Under drought, decreasing water availability results in reduced leaf water potentials and a sequence of physiological responses including reduced photosynthesis, growth rate, and ultimately, fitness (Taiz and Zeiger, 2014). Plants therefore seek to maintain homeostasis of leaf water potential, with the highest (least negative) values supporting the most efficient functioning of photosynthesis and other metabolic processes in most species (Lawlor and Fock, 1978; Turner and Begg, 1981; Kramer and Boyer, 1995; Cornic and Massacci, 1996; Jones, 2007). Plants that exhibit dehydration avoidance strategies compensate for soil water deficit through phenotypic plasticity of gene expression (Verslues et al., 2006; DesMarais and Juenger, 2010; DesMarais et al., 2013; Lovell et al., 2015) and downstream physiological phenotypes (Levitt, 1980), among others.To understand plant stress responses, it is critical to determine the physiological and genetic underpinnings of drought adaptation in both field and laboratory conditions (Travers et al., 2007; Gaudin et al., 2013). A common finding among such studies is that physiological and gene expression responses to drought vary considerably depending on the severity and temporal dynamics of drying soil (Chaves et al., 2003; Barker et al., 2005; Malmberg et al., 2005; Mittler, 2006; Mishra et al., 2012). Natural soil moisture variation, which has shaped adaptive responses to drought in wild populations, is not necessarily recapitulated by controlled (often, “shock”) laboratory experiments. For example, single abiotic stresses rarely occur in isolation in the field (Mittler, 2006). Instead, wild and crop plants respond to the combination of diverse stressors such as drought, heat, and salinity, simultaneously and at both molecular (e.g. Rizhsky et al., 2002; Rizhsky et al., 2004; Suzuki et al., 2005) and physiological (e.g. Heyne and Brunson, 1940; Craufurd and Peacock, 1993; Machado and Paulsen, 2001) levels. Therefore, inquiries into evolved plant stress responses are perhaps best served by experimental conditions that emulate selective agents in the field. Given that the extent and severity of stress causes qualitatively different physiological responses, it is not surprising that several studies have found relatively weak genetic correlations between laboratory phenotypes and those collected in the field (e.g. Weinig et al., 2002; Malmberg et al., 2005; Anderson et al., 2011; Mishra et al., 2012).Soil properties and biota can also affect plant growth and physiology (Meisner et al., 2013; Schweitzer et al., 2014), which may be exacerbated by contrasts between growth in potting mix or in native soil (Rowe et al., 2007; Heinze et al., 2016). The observation that field-grown plants have different root systems and greater total water storage than those in greenhouse pots is of particular importance to water relations (Poorter et al., 2012a). Short-term drought stress in the field may be buffered by access to larger volumes of soil and more complex root-soil-water dynamics, conditions poorly represented in most controlled settings.The field of experimental design has been fundamentally shaped by a central problem of biology: that it is notoriously difficult to control environmental factors in the field (Jones, 2013). A classic solution is to increase biological replication, but this is generally not feasible with costly and time-sensitive physiological and genetic assays (Poorter et al., 2012b; Marchand et al., 2013). Despite these difficulties, understanding the effects of drought in field conditions is necessary because it is in these settings that yield is impacted and selection is acting to shape adaptive responses to stress. Here, we determine how the interplay between drought severity, planting condition (e.g. field, potted, greenhouse) and sampling timing impacts physiological and genomic responses to drought in the C₄ perennial grass, Panicum virgatum (switchgrass). To accomplish this, we used observations collected from clonally replicated individuals of the “AP13” switchgrass genotype (derived from the Alamo cultivar), which is the genome reference for this important biofuel crop and dominant member of mesic tall grass prairie ecosystems. The Alamo cultivar is a southern lowland accession that has high vigor and performance across a variety of climatic conditions. Replicates were grown in three separate soil moisture manipulation experiments with distinct rooting environments: in medium sized pots in a greenhouse, in large containers in a field setting, and in native soil under rainout shelters. In all three of these experiments, we collected leaf-level physiological and whole-genome gene expression data from droughted and control plants.Combined, the three experiments represent contrasts in drought experimental manipulations (i.e. the extent, timing, and duration of drought), plant characteristics (i.e. age, maturity, and size), and broadly fit with the concepts of best practice for physiological analysis of drought responses (Poorter et al., 2012b). Contrasting these experimental design considerations allows us to address how edaphic and climactic conditions impact links between gene expression and physiological phenotypic plasticity. Specifically, we assessed three fundamental questions pertaining to physiological genomics in the field: (1) How consistent is phenotypic plasticity to drought across experiments? (2) Which soil moisture deficit responses vary across sites, years, and timing of sampling? (3) How does plasticity of physiological and gene expression phenotypes covary within and across experiments? To assess these questions, we tested how leaf physiology and whole-genome gene expression responded to the effects of drought treatments, leaf water potential, and sampling time (midday and predawn). These analyses permitted inference of the number, relative effect size, and identity of differentially expressed (plastic) genes. Overall, our results suggested that differences in leaf water potential and diurnal patterns were the major drivers of gene expression variation. Furthermore, we observed consistent physiological plasticity across greenhouse dry-down and field precipitation manipulation experiments, but extreme variability in the number of differentially expressed genes.     

Population Changes of Soil Microbial Communities Induced by Hydrocarbon and Heavy Metal Contamination

Substrate utilization tests with Biolog® plates were used to obtain information on shifts in community composition and on changes in the metabolic diversity and activity of microorganisms in soil polluted with hydrocarbons. and/or heavy metals. Differences between the patterns of substrate utilization of endogenous microorganisms of pristine and contaminated soils were investigated by multivariate analysis. Population changes and shifts in metabolic diversity were observed both after hydrocarbon pollution or heavy metal contamination. The overall activity on the 95 Biolog® Gram-negative (GN) substrates correlated well with the respiration rate of the soil. Soils contaminated with hydrocarbons showed higher metabolic potentials than the corresponding controls. In contrast, heavy metal pollution caused both lower metabolic activity and a loss in diversity. The Biolog® assay was found to be suitable to describe changes in functional diversity of soils caused by hydrocarbon contamination or heavy metal stress.     

Brief communication: Investigation of the semicircular canal variation in the Krapina Neandertals

Previous studies comparing bony labyrinth morphology in geographically‐dispersed samples of Neandertals and modern Homo sapiens (H. sapiens) showed that Neandertals generally have smaller semicircular canals than modern H. sapiens (Hublin et al., 1996 ; Spoor et al., 2003 ; Glantz et al., 2008 ). Here we analyze the morphology of a single group of Neandertal specimens from one locale, the Krapina site, to determine the intraspecific variation in Neandertal semicircular canal sizes. Dimensions of the semicircular canals were collected from computed tomography scans of nine temporal bones. With the rare exception, the dimensions of the semicircular canals in the Krapina sample are similar to those previously reported across a geographically‐dispersed sample of Neandertals, further supporting previous studies that suggest low levels of variation in the semicircular canals for Neandertals. Am J Phys Anthropol 154:302–306, 2014. © 2014 Wiley Periodicals, Inc.     

Microbial Degradation of Organic Pollutants in Soil in a Cold Climate

Cold-adapted microorganisms are potentially interesting for use in environmental biotechnology applications since a large part of the biosphere has low temperatures during at least parts of the year. Many studies have shown that both oil-contaminated and uncontaminated soils in the Arctic, the Antarctic and the Alps contain microbes that can degrade different hydrocarbons deriving from oils. A few studies have also been conducted on degradation of herbicides in soils at low temperatures. Furthermore, phenols and some polychlorinated biphenyl (PCB) congeners have proved to be degradable at low temperatures, using microorganisms isolated from sediments or soils. Additions of nitrogen and phosphorous to polluted soils have been shown to enhance the degradation of hydrocarbons in many cases. Bioaugmentation with hydrocarbon degrading cold-adapted microorganisms has given varying results. The inoculated microorganisms have probably been out-competed by the indigenous microorganisms in some cases. Different ways to increase the efficiency of microbial degradation of organic pollutants in soil in a cold climate is discussed.     

Putting the genes into community genetics

As part of the long‐term fusion of evolutionary biology and ecology (Ford, 1964), the field of community genetics has made tremendous progress in describing the impacts of plant genetic variation on community and ecosystem processes. In the “genes‐to‐ecosystems” framework (Whitham et al., 2003), genetically based traits of plant species have ecological consequences, but previous studies have not identified specific plant genes responsible for community phenotypes. The study by Barker et al. (2019) in this issue of Molecular Ecology uses an impressive common garden experiment of trembling aspen (Figure 1) to test for the genetic basis of tree traits that shape the insect community composition. Using a Genome‐Wide Association Study (GWAS), they found that genomic regions associated with phytochemical traits best explain variation in herbivore community composition, and identified specific genes associated with different types of leaf‐modifying herbivores and ants. This is one of the first studies to identify candidate genes underlying the heritable plant traits that explain patterns of insect biodiversity.