Laboratory Microcosm Studies Research Articles

Response of Microbial Communities to Naturally Occurring Radioactive Material-Contaminated Sediments: A Microcosm-Based Study.

There is a growing need to understand the potential ecological impacts of contaminants in offshore oil and gas infrastructure, especially if that infrastructure is to be left in situ as a decommissioning option. Naturally occurring radioactive material (NORM) is one type of contaminant found in solid deposits on internal surfaces of infrastructure that poses potential ecological harm if released into the marine environment. Microbes are important components of marine sediment ecosystems because they provide ecosystem services, yet the impacts of NORM contamination to these communities are not well understood. The present study aimed to investigate the response of benthic microbial communities to NORM-contaminated scale, collected from an offshore oil and gas system, via controlled laboratory microcosm studies. Changes to microbial communities in natural sediment and sediments spiked with NORM at radium-226 activity concentrations ranging from 9.5 to 59.8 Bq/kg (in partial equilibria with progeny) over 7 and 28 days were investigated using high-throughput sequencing of environmental DNA extracted from experimental sediments. There were no significant differences in microbial community composition between control and scale-spiked sediments over 7 and 28 days. However, we observed a greater presence of Firmicutes in the scale-mixed treatment and Chloroflexi in the scale-surface treatments after 28 days. This could suggest selection for species with contaminant tolerance or potential resilience to radiation and metal toxicity. Further research is needed to explore microbial tolerance mechanisms and their potential as indicators of effects of radionuclide-contaminated sediments. The present study demonstrated that microcosm studies can provide valuable insights about the potential impacts of contamination from oil and gas infrastructure to sediment microbial communities. Environ Toxicol Chem 2024;43:1648-1661. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Unveiling the impact of microplastics with distinct polymer types and concentrations on tidal sediment microbiome and nitrogen cycling

Microplastics (MPs) are distributed widely in the ocean surface waters and sediments. Increasing MPs contamination in intertidal zone profoundly impacts microbial ecosystem services and biogeochemical process. Little is known about the response of tidal sediment microbiome to MPs. We conducted a 30-day laboratory microcosm study using five polymers (PE, PBS, PC, PLA and PET) at three concentrations (1 %, 2 % and 5 %, w/w). High throughput sequencing of 16 S rRNA, qPCR and enzyme activity test were applied to demonstrate the response of microbial community and nitrogen cycling functional genes to MPs. MPs reduced the microbial alpha diversity and the microbial dissimilarity while the effects of PLA-MPs were concentration dependent. LEfSe analysis indicated that the Proteobacteria predominated for all MP treatments. Mantel’s test, RDA and correlation analysis implied that pH may be the key environmental factor for causing microbial alterations. MPs enhanced nitrogen fixation in tidal sediment. PLA levels of 1 % but not 5 % produced the most significant effects in nitrogen cycling functional microbiota and genes. PLS-PM revealed that impacts of MPs on tidal sediment microbial communities and nitrogen cycling were dominated by indirect effects. Our study deepened understanding and filled the knowledge gap of MP contaminants affecting tidal sediment microbial nitrogen cycling.

Efficacy of amorphous TiOx-coated surfaces against micro- and macrofouling through laboratory microcosms and field studies

In this study, Soda Lime Glass (SLG) and Stainless Steel (SS316L) substrata coated with Titanium oxide (TiOx) were tested for their efficacy in the laboratory microcosms and in field against micro- and macrofouling. Laboratory microcosm studies were conducted for five days using natural biofilms, single-species diatom (Navicula sp.), and bacterial biofilms, whereas field observations were conducted for 30 days. The TiOx-coating induced change in the mean contact angle of the substratum and rendered SS316L more hydrophilic and SLG hydrophobic, which influenced the Navicula sp. biofilm, and bacterial community structure of the biofilm. Overall, the TiOx-coated SS316L showed minimal microfouling, whereas non-coated SLG exhibited greater efficacy in deterring/preventing macrofouling organisms. Moreover, the reduction in macrofouling could be attributed to high abundance of Actinobacteria. Unraveling the mechanism of action needs future studies emphasizing biochemical processes and pathways.

The effect of Paenibacillus on IDEXX Enterolert results from freshwater stream environments.

Enterolert, a fluorogenic substrate test, is used as a quantitative method for determining freshwater concentrations of Enterococcus for water quality indicators. However, there is some evidence from recent studies suggesting that Enterolert may not suppress false positives due to pollution sources in waterbodies. In this study, we evaluated this method by analyzing field water and sediment samples from four freshwater streams. We also performed a laboratory microcosm study from two of the stream sediments. The Enterolert method was investigated by phenotypic and genomic analyses for accuracy of isolating and quantifying Enterococcus and/or Streptococcus. Additionally, we tested isolates from Enterolert panels for antibiotic resistance. Results from the field and microcosm studies from initial to final time points indicated that false positives were predominantly Paenibacillus spp. and other non-fecal indicator bacteria. Furthermore, the microcosm study indicated shifts from lactic acid to non-lactic acid bacteria between initial to final time points, but Enterococcus concentrations from Enterolert panels remained stable for the duration of the study for both stream sediments. Antibiotic resistance indicated no distinct pattern of resistance or susceptibility to a suite of antibiotics. However, all isolates tested were resistant to bacitracin and nalidixic acid. In conclusion, we found that Enterolert was not exclusively selective for Enterococcus from freshwater environments and that sediment and polluted waterbodies have the potential to skew the presumed concentrations. More research is needed to evaluate the effectiveness and selectivity of the medium used for the fluorogenic substrate test for Enterococcus enumeration.

Biodegradation of hydrocarbons from contaminated soils by microbial consortia: A laboratory microcosm study

BackgroundCompounds derived from hydrocarbons are essential for industry and our daily life; however, accidents such as spills or leaks occur regularly, causing severe environmental impact. Therefore, bacteria isolated from an oil well were characterized to assess their potential in the degradation of hydrocarbons under individual and consortium treatments. Soil samples, from a well contaminated with hydrocarbons in Tabasco, Mexico, were collected. The biosurfactant, emulsifying capacity, hemolytic activity, ionic charge, and biofilm formation were analyzed. ResultsMost of the isolated strains belong to the genus Pseudomonas according to 16S rDNA sequencing. In general, emulsification percentages greater than 60% in the different substrates evaluated were observed. In addition, these strains can form biofilms, and those selected to integrate the microbial consortia present anionic surfactants. Three strains were selected to evaluate the degradation potential of soil contaminated with hydrocarbons from the same site where the bacteria were isolated in a microcosm. The microbial consortia degraded the contaminated soil more efficiently than the strains were evaluated alone, mainly the three bacteria consortia, with percentages greater than 80%. ConclusionsThis study shows that, despite belonging to the same species, bacterial strains’ metabolic capacity for the expression of surfactant compounds, emulsifiers, and the formation of biofilms are different. Furthermore, the more structured a community is, the greater the biodegradation process that occurs when bacteria act individually on the substrate. Therefore, this study demonstrates that strains of the same species integrated microbial consortia improve the bioremediation processes of hydrocarbons in contaminated soils.How to cite: Lázaro-Mass S, Gómez-Cornelio S, Castillo-Vidal M, et al. Biodegradation of hydrocarbons from contaminated soils by microbial consortia: A laboratory microcosm study. Electron J Biotechnol 2023;61. https://doi.org/10.1016/j.ejbt.2022.10.002.

Factors Affect the Sorption and Degradation of and Rostenedione in Three Typical Agricultural Soils From Different Regions

Androstenedione is a natural steroid hormone and endocrine disruptor. Batch and laboratory microcosm experiments and studies were conducted to investigate its adsorption and degradation in three soils. The Freundlichparameter Kf of androstenedione in the tested soils. Cattle manure dissolved organic matter (DOM) at 20 mg C·L−1 decreased androstenedione sorption in the three soils Degradation rate positively correlated with content clay and silt, while negatively with content of sand under same conditions. Soil moisture significantly affected the persistence of androstenedione in red soil and black soil, whereas there was no significant difference in alluvial soil. Androstenedione half-life increased, ranging from 2.04d to 17.33d under soil temperatures of 20°C,10°C, and freeze-thaw cycles between +10°C and−10°C. Androstenedione degradation was inhibited in black soil at -10°C. Androstenedione degradation significant affected by soil texture and environmental factors, manure DOM inhibitedandrostenedione sorption in three soils and can increase its transport to water sources.

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. A similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.

Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential

Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.

Impact of underground storm drain systems on larval ecology of Culex and Aedes species in urban environments of Southern California

An extensive network of storm water conveyance systems in urban areas, often referred to as the “underground storm drain system” (USDS), serves as significant production habitats for mosquitoes. Knowledge of whether USDS habitats are suitable for newly introduced dengue vectors Aedes aegypti and Ae. albopictus will help guide surveillance and control efforts. To determine whether the USDS functions as a suitable larval habitat for Culex, Ae. aegypti and Ae. albopictus in southern California, we examined mosquito habitat utilization and larval survivorship using laboratory microcosm studies. The data showed that USDS constituted 4.1% of sampled larval habitats for Ae. aegypti and Ae. albopictus, and 22.0% for Cx. quinquefasciatus. Furthermore, USDS water collected in the summer completely inhibited Aedes larval development, but yielded a 15.0% pupation rate for Cx. quinquefasciatus. Food supplementation in the microcosms suggests that nutrient deficiency, toxins and other factors in the USDS water led to low success or complete failure of larval development. These results suggest that USDS habitats are currently not major productive larval habitats for Aedes mosquitoes in southern California. Our findings prompt inclusion of assessments of pupal productivity in USDS habitats and adult mosquito resting sites in the mosquito surveillance program.

Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions.

Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.

Ageing effect on conazole fungicide bioaccumulation in arable soils

Widely used conazole fungicides (CFs) belong to the most frequently detected pesticides in Central European arable soils. However, data on their environmental behaviour and bioavailability to soil organisms are surprisingly scarce. In the present laboratory microcosm study prochloraz, tebuconazole, epoxiconazole and flusilazole were applied to 12 different agricultural soils at background levels. Bioaccumulation to earthworm E. andrei and lettuce L. sativa roots and leaves was evaluated in non-aged (biota exposure after addition of pesticides) and aged (exposure started three months later) systems. In contrast with expectations from ageing effect (decrease of bioavailability), bioaccumulation in E. andrei was both reduced and enhanced after ageing depending on soil properties. The reduction of bioaccumulation correlated positively to the percentage of clay but negatively to soil organic matter. The affinity of compost worm E. andrei towards organic matter where hydrophobic pesticide molecules are sorbed is discussed as a possible explanation. An apparent effect of ageing (reduction of bioavailability) was particularly observed in lettuce roots, where bioaccumulation was significantly reduced in time. However, bioaccumulation in leaves changed ambiguously in aged variants among CFs, possibly as a combined result of bioconcentration, dilution by plant growth and metabolism. This study brings first insights into how the bioaccumulation of conazole fungicides is affected by sequestration in agricultural soils. The results indicate that in complex systems, the ageing is not necessarily connected with decrease of bioaccumulation.

Greenhouse gas emissions from intact riparian wetland soil columns continuously loaded with nitrate solution: a laboratory microcosm study.

In this study, we aimed at determining greenhouse gas (GHG) (CO2, CH4, and N2O) fluxes exchange between the soil collected from sites dominated by different vegetation types (Calamagrostis epigeios, Phragmites australis, and Carex schnimdtii) in nitrogenous loaded riparian wetland and the atmosphere. The intact soil columns collected from the wetland were incubated in laboratory and continuously treated with [Formula: see text]-enriched water simulating downward surface water percolating through the soil to become groundwater in a natural system. This study revealed that the soil collected from the site dominated by C. epigeios was net CO2and N2O sources, whereas the soil from P. australis and C. schnimdtii were net sinks of CO2and N2O, respectively. The soil from the site dominated by C. schnimdtii had the highest climate impact, as it had the highest global warming potential (GWP) compared with the other sites. Our study indicates that total organic carbon and [Formula: see text] concentration in the soil water has great influence on GHG fluxes. Carbon dioxide (CO2) and N2O fluxes were accelerated by the availability of higher [Formula: see text] concentration in soil water. On the other hand, higher [Formula: see text] concentration in soil water favors CH4 oxidation, hence the low CH4 production. Temporally, CO2 fluxes were relatively higher in the first 15 days and reduced gradually likely due to a decline in organic carbon. The finding of this study implies that higher [Formula: see text] concentration in wetland soil, caused by human activities, could increase N2O and CO2 emissions from the soil. This therefore stresses the importance of controls of [Formula: see text] leaching in the mitigation of anthropogenic N2O and CO2 emissions.

Genetic and physiological characterisation of phenol- and p-cresol-degrading bacteria selected for bioaugmentation in oil- and phenol-polluted area

Successful bioaugmentation requires that bacterial strains introduced into the polluted area must be able to adapt to new environmental conditions and retain high enough catabolic activity. The strains should degrade pollutant present at high concentrations, while having high affinity for the pollutants for their thorough degradation. The transfer of genetic information from introduced donor strain to indigenous bacterial population increases the biodegradation potential. As laboratory-selected strains can be poor survivors and lose catabolic activity in mixed microbial ecosystems, the indigenous biodegradative strains isolated from the river water continuously polluted with phenolic compounds of oil shale leachate may serve as inoculants for bioaugmentation. We have shown that the native phenol- and p-cresol-degrading community could be grouped according to the presence of catabolic genes involved in catabolism of aromatic compounds. The selected representative strains of different catabolic types of degradation of phenol and p-cresol were identified as Pseudomonas mendocina (strain PCl) and P. jluorescens (strains PC! 8, PC24). Catabolic potential of these strains was studied on the basis of phenol hydroxylase, p-cresol methylhydroxylase and catechol 2,3-dioxygenase genes. The occurrence and conjugation of plasmid DNA were revealed in these strains. The ability of the selected strains to degrade several phenolic compounds in natural phenolic wastewater in which the compounds were present in multicomponent mixtures, was investigated through laboratory microcosm studies, To elucidate the extent of interactions among the used bacterial strains single and mixed cultures were set up. The biodegradation activity of strains in microcosms was examined through viable counts, consumption of phenolic compounds and detecting the presence of catabolic genes by hybridization, During the experiments (30 days) the introduced bacteria remained viable even when the substrates were depleted. The mixture of strains was more effective in the decomposition of phenolic compounds from the natural wastewater as compared with the single culture conditions and the metabolic activity and cell density of each strain were co-ordinated within a specific time scale. The behaviour of strains in the phenolic leachate depended on the growth kinetics of the strains (K,,µ).

Rapid formation of iron sulfides alters soil morphology and chemistry following simulated marsh restoration

Many marshes show signs of degradation due to fragmentation, lack of sediment inputs, and erosion which may be exacerbated by sea level rise and increasing storm frequency/intensity. As a result, resource managers seek to restore marshes via introduction of sediment to increase elevation and stabilize the marsh platform. Recent field observations suggest the rapid formation of iron sulfide (FeS) materials following restoration in several marshes. To investigate, a laboratory microcosm study evaluated the formation of FeS following simulated restoration activities under continually inundated, simulated drought, and simulated tidal conditions. Results indicate that FeS horizon development initiated within 16 days, expanding to encompass >30% of the soil profile after 120 days under continuously inundated and simulated tidal conditions. Continuously inundated conditions supported higher FeS content compared to other treatments. Dissolved and total Fe and S measurements suggest the movement and diffusion of chemical constituents from native marsh soil upwards into the overlying sediments, driving FeS precipitation. The study highlights the need to consider biogeochemical factors resulting in FeS formation during salt marsh restoration activities. Additional field research is required to link laboratory studies, which may represent a worst case scenario, with in-situ conditions.

Dynamics of seagrass bed microbial communities in artificial Chattonella blooms: A laboratory microcosm study

The influence of algicidal and growth-inhibiting bacteria in a seagrass (Zostera marina) bed, and their capability of controlling blooms of the fish-killing raphidophyte flagellate, Chattonella antiqua, were examined in laboratory microcosm experiments. Bacterial communities in seawater collected from the seagrass bed and Z. marina biofilm suppressed artificial Chattonella blooms in the presence of their natural competitors and predators. Phylogenetic analysis suggest that considerable numbers of bacteria that suppress Chattonella, including algicidal or growth-inhibiting bacteria isolated from seagrass biofilm and seawater from the seagrass bed, are members of Proteobacteria that can decompose lignocellulosic compounds. A direct comparison of partial 16S rRNA gene sequences (500 bp) revealed that the growth-limiting bacterium (strain ZM101) isolated from Z. marina biofilm belonged to the genus Phaeobacter (Alphaproteobacteria) showed 100% similarity with strains of growth-limiting bacteria isolated from seawater of both the seagrass bed and nearshore region, suggesting that the origin of these growth-limiting bacteria are the seagrass biofilm or seawater surrounding the seagrass bed. This study demonstrates that Chattonella growth-limiting bacteria living on seagrass biofilm and in the adjacent seawater can suppress Chattonella blooms, suggesting the possibility of Chattonella bloom prevention through restoration, protection, or introduction of seagrass in coastal areas.

Degradation Kinetics and Transformation Products of Levonorgestrel and Quinestrol in Soils.

Levonorgestrel (LNG) and quinestrol (QUN) are typical endocrine disruptors that enter the soil via sewage irrigation and sludge return. However, the fates of both compounds in soil are not well-understood. Laboratory microcosm studies were conducted to fill the gap of understanding of LNG and QUN behavior in soils. High values of goodness-of-fit indices (GFIs) were obtained using the double-first-order in parallel (DFOP) model and the single-first-order (SFO) model to fit the degradation kinetics of LNG and QUN in soils, respectively. The end-points (DT50 and DT90) of LNG and QUN were positively correlated with soil total organic carbon (TOC). Soil water content and temperature were observed to be critical factors in degradation of LNG and QUN. The degradation rates of LNG and QUN were very slow under sterile and flooded conditions, indicating that the aerobic microbial degradation was dominant in the degradation of LNG and QUN. Moreover, major transformation products were identified, and biodegradation pathways of LNG and QUN were proposed. The present study is expected to provide basic information for ecological risk assessment of LNG and QUN in the soil compartment.

Autonomous screening of groundwater remediation technologies in the subsurface using the In Situ Microcosm Array (ISMA).

The groundwater remediation industry continues to progress towards less expensive, more sustainable in situ remedies. However, in situ treatment requires site-specific performance data that can be difficult or impossible to obtain using conventional laboratory microcosm studies. To improve the representativeness of laboratory scale treatability studies, and aid in remedial technology implementation, we developed the In Situ Microcosm Array (ISMA). This autonomous diagnostic device enables the deployment of 10 flow-through sediment columns within a standard 10-cm groundwater-monitoring well. Suspended at the desired aquifer depth, the fully encapsulated ISMA meters groundwater directly from the aquifer to microcosms containing competing remedial technologies. Field demonstrations of the instrument were performed in two aquifers contaminated, respectively, with trichloroethylene and hexavalent chromium, and with perchlorate. A cost assessment positions ISMA deployment costs within the range of conventional laboratory treatability studies. Results demonstrate the ISMA's utility to perform cost-effective, high-throughput, screenings of multiple intervention strategies in the field, without impacting the subsurface environment examined.

A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes.

Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing. Members of the Dehalobacter and Dehalococcoides are reported to respire chlorobenzenes; however, neither were abundant in our sediment microcosms. Instead, we observed a significant increase in the relative abundance of Dehalogenimonas from <1% to 16-30% during dechlorination of 1,2,4-trichlorobenzene (TCB), 1,2-dichlorobenzene (DCB), and 1,3-DCB over 19 months. Quantitative PCR (qPCR) confirmed that Dehalogenimonas gene copies increased by 2 orders of magnitude with an average yield of 3.6 ± 2.3 g cells per mol Cl- released ( N = 12). In transfer cultures derived from sediment microcosms, dechlorination of 1,4-DCB and monochlorobenzene (MCB) was carried out by Dehalobacter spp. with a growth yield of 3.0 ± 2.1 g cells per mol Cl- released ( N = 5). Here we show that a Dehalogenimonas population respire 1,2,4-TCB and 1,2-/1,3-DCB isomers. This finding emphasizes the need to monitor a broader spectrum of organohalide-respiring bacteria, including Dehalogenimonas, at sites contaminated with halogenated organic compounds.

Growth rate of alpine phytoplankton assemblages from contrasting watersheds and N‐deposition regimes exposed to nitrogen and phosphorus enrichments

Abstract High mountain lakes are a network of sentinels, sensitive to any events occurring within their waterbodies, their surrounding catchments and their airsheds. By modifying nutrient balance and availability in water, both local and global changes are expected to alter primary productivity and to trigger strong ecological impacts in these ecosystems. Predicting ecological trajectories under future change is a key challenge for both scientists and conservation managers. French alpine lakes, in the most southern and western part of the European Alps, have received surprisingly little attention to date. In this article, we address how variations in nitrogen (N) and phosphorus (P) supply are likely to impact the area's phytoplankton growth. We performed N and/or P enrichment microcosm experiments under controlled conditions on 12 phytoplankton assemblages sampled during the summer 2016 in four French alpine lakes with contrasting catchments and N‐deposition regimes. The nutrients limiting phytoplankton growth varied according to the nutrient stoichiometry of the lake water. In the lakes exposed to high N‐deposition rates (≈700 kg N km–2 year–1), the water contained more N than P and phytoplankton growth in microcosms was either limited by P or not limited by either N or P. In the lakes exposed to low N‐deposition rates (≈500 kg N km–2 year–1), N availability relative to P was lower in the lake with vegetated catchment than in the lake with rocky catchment, resulting in a switch from P to NP colimitation of the phytoplankton in microcosms. Our data clearly indicate that French alpine lakes do not host the same diversity and structure of phytoplankton communities and that phytoplankton composition influenced phytoplankton growth in microcosms. First, we show that nonmotile colonial chlorophytes appeared in late summer assemblages, with lower growth rates but P‐storage abilities. Second, our findings indicate that the growth of phytoplankton assemblages dominated by diatoms was increasingly limited by silica (SiO2) throughout the summer, along with a 70% decrease in SiO2 concentration in lake water. The forecast global changes in the French Alps should increase phytoplankton growth in most high mountain lakes where P is the main limiting nutrient, before NP colimitation. These changes are likely to be of lesser extent in lakes with large vegetated catchments in the northern area with lower N‐deposition rates and of greater extent in the southern area with higher N‐deposition rates and future P‐deposition rates. By investigating the relationship between nutrient availability, phytoplankton composition and phytoplankton growth rate, this experimental laboratory microcosm study will help interpret current multifactorial data from in situ monitoring networks in the Alps. It will also be helpful to develop models to better predict the sentinel lake responses to local and global changes.

Pesticide residues remaining in soils from previous growing season(s) - Can they accumulate in non-target organisms and contaminate the food web?

Epoxiconazole, tebuconazole, flusilazole, prochloraz, pendimethalin, and the atrazine transformation product (2-hydroxyatrazine) have been found in Czech arable soils at high detection frequencies and/or concentrations. As they have been shown to persist from one growing season to following ones, the question arises of whether they can be taken up by non-target soil organisms and by subsequently planted crops. To reveal this, soils field-contaminated with pesticide residues were subjected to laboratory microcosm studies to measure i) dissipation rates, ii) accumulation in earthworms and lettuce, and iii) exposure by means of solid-phase microextraction (SPME). In parallel, tests with a freshly laboratory-contaminated soil were performed and represented the worst case scenario to be compared with. It was observed that at the residual levels (≤0.1 mg/kg), the behavior of field aged and fresh residues was similar, except for bioaccumulation in earthworms that was significantly lower for aged residues than for fresh residues. Residues' potential for bioconcentration was generally low, i.e., below the maximum residue limits (MRLs) of lettuce. This is in line with SPME results showing low levels of exposure via soil porewater. It follows that these pesticide residues are not likely to pose significant threats to the soil environment, the food web and, consequently, human health if present in soils at levels of ≤0.1 mg/kg.