Assessment of self-organizing maps to analyze sole-carbon source utilization profiles

Thermal history influences the recovery of phototrophic biofilms exposed to agricultural run-off in intermittent rivers

The response of microbial communities to disturbances may be controlled by the past environmental conditions, through their legacy effect. In intermittent rivers, the fixed microorganisms, such as phototrophic biofilms, are exposed to variable environmental conditions, including changes in water chemistry, hydrodynamics and, in some cases water temperature. The latter may be particularly affected by the increasing frequency of summer heat waves. Our objective was therefore to assess the legacy effect of warming on phototrophic biofilms during a flow intermittency sequence. Our main hypotheses were that the thermal history of biofilms determines (i) the community trajectory after rewetting and (ii) its resistance and resilience to a new disturbance. To test these hypotheses, we exposed phototrophic biofilms grown in the lab to a flow intermittency sequence (1 week no flow / 12 weeks no water) at two contrasted temperatures (22 °C and 32 °C). After rewetting (22 °C), some of the biofilms were exposed for 1 week to a new disturbance, i.e. a contaminant mimicking agricultural run-off (nitrate, copper, insecticide, herbicide, fungicide). The structure (pigments, elementary composition, extracellular polymeric substances, prokaryotic composition) and functioning (respiration, photosynthesis, functional diversity) of the biofilms were measured at the end of the contamination, and after 1 and 3 weeks of recovery without contaminant. Our results unexpectedly show that one week after rewetting the "warmed" biofilms were less heterotrophic than the "non-warmed" biofilms. This effect was transitory, although the prokaryotic composition of the biofilms still diverged 4 weeks after rewetting. The legacy effect of warming was an increased sensitivity of the biofilms to the complex contaminant, especially at the highest concentrations. This legacy effect decreased with time for the general structure and functioning of the biofilms, but persisted for the prokaryotic composition. These findings highlight the importance of historical conditions, and particularly thermal history, in the ability of microbial communities to respond to disturbances.

A new strategy of using periphyton to simultaneously promote remediation of PAHs-contaminated soil and production of safer crops

Contaminated farmland leads to serious problems for human health through biomagnification in the soil-crop-human chain. In this paper, we have established a new soil remediation strategy using periphyton for the production of safer rice. Four representative polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (Phe), pyrene (Pyr), benzo[b]fluoranthene (BbF), and benzo[a]pyrene (BaP), were chosen to generate artificially contaminated soil. Pot experiments demonstrated that in comparison with rice cultivation in polluted soil with ΣPAHs (50 mg kg-1) but without periphyton, adding periphyton decreased ΣPAHs contents in both rice roots and shoots by 98.98% and 99.76%, respectively, and soil ΣPAHs removal reached 94.19%. Subsequently, risk assessment of ΣPAHs based on toxic equivalent concentration (TEQ), pollution load index (PLI), hazard index (HI), toxic unit for PAHs mixture (TUm), and incremental lifetime cancer risk (ILCR) indicated that periphyton lowered the ecological and carcinogenicity risks of PAHs. Besides, the role of periphyton in enhancing the rice productivity was revealed. The results indicated that periphyton alleviated the oxidative stress of PAHs on rice by reducing malondialdehyde (MDA) content and increasing total antioxidant capacity (T-AOC). Periphyton reduced the toxic stress of PAHs on the soil by promoting soil carbon cycling and metabolic activities as well. Periphyton also improved the soil's physicochemical properties, such as the percentage of soil aggregate, the contents of humic substances (HSs) and nutrients, which increased rice biomass. These findings confirmed that periphyton could improve rice productivity by enhancing soil quality and health. This study provides a new eco-friendly strategy for soil remediation and simultaneously enables the production of safe crops on contaminated land.

Iodine distribution and volatilization in contrasting forms of forest humus during a laboratory incubation experiment

Radionuclides ¹²⁹I (t_1/2 = 15.7 × 10⁶ years) and ¹³¹I (t_1/2 = 8.02 days) are both introduced into the environment as a result of nuclear human activities. Environmental transfer pathways and fluxes between and within ecosystems are essential information for risk assessment. In forest ecosystems, humus degradation over time could result in re-mobilization and then downward migration and/or volatilization of intercepted ¹²⁹I. In order to estimate the scale of these processes, humus (mull and moder forms) sampled under deciduous and coniferous forests were spiked with ¹²⁵I^- (t_1/2 = 59.4 days), as a surrogate for ¹²⁹I, in order to study the evolution of its water-soluble and organic fractions as well as the volatilization rate during humus degradation at laboratory scale. To our knowledge, this is the first time that interactions between iodine and contrasting forms of forest humus have been investigated. The evolution of native stable iodine (¹²⁷I) pools in unspiked humus was also studied. The nature of the humus' organic matter appears to be a factor that impacts on the proportions of water-soluble and organic fractions of iodine and on their evolution. Iodine-125 was mainly organically bound (fraction for mulls and moders: ∼54-59 and 41-49%, respectively) and no clear evolution was observed within the 4-month incubation period. A large decrease in ¹²⁵I water-solubility occurred, being more marked for mull (from ∼14-32 to 3-7%) than for moder (from ∼21-37 to 7-19%) humus. By contrast, a significant fraction was not extractible (∼38-43%) and varied in inverse proportion to the water-soluble fraction, suggesting a stabilization of iodine in humus after wet deposit. The nature of the humus organic matter also impacted on ¹²⁵I volatilization. Although of the same order of magnitude, the total volatilization of ¹²⁵I was higher for moders (∼0.039-0.323%) than for mulls (∼0.015-0.023%) within the 4-month incubation period. Volatilization rates for mulls were correlated with the water-soluble fraction, implying that volatilization of ¹²⁵I could occur from the humus solution. Our results showed that humus is thus a zone of iodine accumulation by association with organic matter and that potential losses by lixiviation are significantly more important compared to volatilization.

Characterizing the long-term occurrence of polycyclic aromatic hydrocarbons and their driving forces in surface waters

As carcinogenic and ubiquitous pollutants, an in-depth understanding of the long-term environmental behaviors of polycyclic aromatic hydrocarbons (PAHs) and their driving forces is crucial for reducing human health risks. Based on long-term monitoring data from 2001 to 2016, this study systematically investigated the temporal and seasonal trends, periodic oscillation, source apportionment, and human health risks of PAHs in eight rivers in the Free State of Saxony, Germany. The results showed that the annual average ∑₁₆PAHs (sum of 16 PAH concentrations) ranged from 28.2 ng L^-1 to 202 ng L^-1. Using the Mann-Kendall test, a trend of decreasing PAH concentrations was determined (slope range: -0.103 to -0.0159). Wavelet analysis indicated that the most significant periodic oscillation of PAHs was 10-30 months, with more pollution in winter. Source apportionment analysis suggested that vehicular emissions and coal combustion contributed the most to PAH concentrations (20.6-40.3% and 21.7-41.4%, respectively) and related health risks (54.1-80.1% and 5.61-37.9%, respectively). Furthermore, the risks (oral lifetime: 4.24×10^-7-1.34×10^-6; dermal lifetime: 2.86×10^-5-9.05×10^-5) were determined to be low. The data revealed that the substitution of petroleum and coal with cleaner energy would facilitate the mitigation of PAHs.

Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility

Fungi cover a range of important ecological functions associated with nutrient and carbon cycling in leaf litter and soil. As a result, research on existing relationships between fungal functional diversity, decomposition rates and competition is of key interest. Indeed, availability of nutrients in soil is largely the consequence of organic matter degradation dynamics. The Biolog^® Phenotype MicroArrays™ (PM) system allows for the testing of fungi against many different carbon sources at any one time. The use and potential of the PM system as a tool for studying niche overlap and catabolic versatility of saprotrophic fungi is discussed here, and examples of its application are provided.

Assessment by self-organizing maps of element release from sediments in contact with acidified seawater in laboratory leaching test conditions

Carbon capture and storage (CCS) is gaining interest as a significant global option to reduce emissions of CO2. CCS development requires an assessment of the potential risks associated with CO2 leakages from storage sites. Laboratory leaching tests have proved to be a useful tool to study the potential mobilization of metals from contaminated sediment in a decreased-pH environment that mimics such a leakage event. This work employs a self-organizing map (SOM) tool to interpret and analyze the release of dissolved organic carbon (DOC), As, Cd, Cr, Cu, Ni, Pb, and Zn from equilibrium, column, and pH-dependent leaching tests. In these tests, acidified seawater is used for simulating different CO2 leakage scenarios. Classification was carried out detailing the mobilization of contaminants for environments of varying pH, liquid-to-solid ratio, and type of contact of the laboratory leaching tests. Component planes in the SOMs allow visualization of the results and the determination of the worst case of element release. The pH-dependent leaching test with initial addition of either base or acid was found to mobilize the highest concentrations of metals.

Resilience of aggregated microbial communities subjected to drought--small-scale studies

The response of microbial communities to disturbance is a major concern for microbial ecologists since potential modifications in their composition and functioning may affect ecosystems to a larger extent. Microbial ecosystems may be resistant (not affected) or may present engineering (return to initial state) or ecological resilience. In the latter case, when the disturbance is released, the ecosystem evolves towards a new equilibrium state. The aim of this study was to determine if variations in the magnitude of a disturbance could induce either engineering or ecological resilience. We used phototrophic biofilms grown in mesocosms as a model of microbial ecosystem and increasing drought duration (1-8 weeks) as a range of disturbances. Biofilm composition (algal and prokaryotic), photosynthetic activity (PhytoPAM), and potential functional diversity (Biolog) were determined at the end of dry phase and after a 2-week rewetting phase in individual aquaria. We only observed an ecological resilience of the biofilm, with a resistance of phototrophic component for the weakest disturbance. After rewetting, the biofilm could fulfill the same functions, but its species composition was highly modified. We observed a shift from cyanobacteria dominance towards diatom dominance. The disturbance caused a transition towards a new steady state of the biofilm. We also observed a positive effect of stress duration on biofilm productivity after resilience.

Effects of nitrogen addition on soil microbes and their implications for soil C emission in the Gurbantunggut Desert, center of the Eurasian Continent

Nitrogen (N) deposition can influence carbon cycling of terrestrial ecosystems. However, a general recognition of how soil microorganisms respond to increasing N deposition is not yet reached. We explored soil microbial responses to two levels of N addition (2.5 and 5 gN m(-2) yr(-1)) in interplant soil and beneath shrubs of Haloxylon ammodendron and their consequences to soil respiration in the Gurbantunggut Desert, northwestern China from 2011 to 2013. Microbial biomass and respiration were significantly higher beneath H. ammodendron than in interplant soil. The responses of microbial biomass carbon (MBC) and microbial respiration (MR) showed opposite responses to N addition in interplant and beneath H. ammodendron. N addition slightly increased MBC and MR in interplant soil and decreased them beneath H. ammodendron, with a significant inhibition only in 2012. N addition had no impacts on the total microbial physiological activity, but N addition decreased the labile carbon substrate utilization beneath H. ammodendron when N addition level was high. Phospholipid fatty acid (PLFA) analysis showed that N addition did not alter the soil microbial community structure as evidenced by the similar ratios of fungal to bacterial PLFAs and gram-negative to gram-positive bacterial PLFAs. Microbial biomass and respiration showed close correlations with soil water content and dissolved carbon, and they were independent of soil inorganic nitrogen across three years. Our study suggests that N addition effects on soil microorganisms and carbon emission are dependent on the respiratory substrates and water availability in the desert ecosystem.

Bacterial community structure in patagonian Andean Lakes above and below timberline: from community composition to community function

Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.

Changes in tolerance to herbicide toxicity throughout development stages of phototrophic biofilms

Ecotoxicological experiments have been performed in laboratory-scale microcosms to investigate the sensitivity of phototrophic biofilm communities to the alachlor herbicide, in relation to the stages of phototrophic biofilm maturation (age of the phototrophic biofilms) and physical structure (intact biofilm versus recolonization). The phototrophic biofilms were initially cultivated on artificial supports in a prototype rotating annular bioreactor (RAB) with Taylor-Couette type flow under constant operating conditions. Biofilms were collected after 1.6 and 4.4 weeks of culture providing biofilms with different maturation levels, and then exposed to nominal initial alachlor concentration of 10 μg L(-1) in either intact or recolonized biofilms for 15 days in microcosms (mean time-weighted average concentration - TWAC of 5.52 ± 0.74 μg L(-1)). At the end of the exposure period, alachlor effects were monitored by a combination of biomass descriptors (ash-free dry mass - AFDM, chlorophyll a), structural molecular fingerprinting (T-RFLP), carbon utilization spectra (Biolog) and diatom species composition. We found significant effects that in terms of AFDM, alachlor inhibited growth of the intact phototrophic biofilms. No effect of alachlor was observed on diatom composition or functional and structural properties of the bacterial community regardless of whether they were intact or recolonized. The intact three-dimensional structure of the biofilm did not appear to confer protection from the effects of alachlor. Bacterial community structure and biomass level of 4.4 weeks - intact phototrophic biofilms were significantly influenced by the biofilm maturation processes rather than alachlor exposure. The diatom communities which were largely composed of mobile and colonizer life-form populations were not affected by alachlor. This study showed that the effect of alachlor (at initial concentration of 10 μg L(-1) or mean TWAC of 5.52 ± 0.74 μg L(-1)) is mainly limited to biomass reduction without apparent changes in the ecological succession trajectories of bacterial and diatom communities and suggested that carbon utilization spectra of the biofilm are not damaged resulting. These results confirmed the importance of considering the influence of maturation processes or community age when investigating herbicide effects. This is particularly important with regard to the use of phototrophic biofilms as bio-indicators.

Assessment of Self-Organizing Map artificial neural networks for the classification of sediment quality

The application of mathematical tools in initial steps of sediment quality assessment frameworks can be useful to provide an integrated interpretation of multiple measured variables. This study reveals that the Self-Organizing Map (SOM) artificial neural network can be an effective tool for the integration of multiple physical, chemical and ecotoxicological variables in order to classify different sites under study according to their similar sediment quality. Sediment samples from 40 sites of 3 estuaries of Cantabria (Spain) were classified with respect to 13 physical, chemical and toxicological variables using the SOM. Results obtained with the SOM, when compared to those of traditional multivariate statistical techniques commonly used in the field of sediment quality (principal component analysis (PCA) and hierarchical cluster analysis (HCA)), provided a more useful classification for further assessment steps. Especially, the powerful visualization tools of the SOM, which offer more information and in an easier way than HCA and PCA, facilitate the task of establishing an order of priority between the distinguished groups of sites depending on their need for further investigations or remediation actions in subsequent management steps.

Use of unsupervised and supervised artificial neural networks for the identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins

Conventional multivariate statistical techniques (hierarchical cluster analysis, linear discriminant analysis) and unsupervised (Kohonen Self Organizing Map) and supervised (Bayesian network) artificial neural networks were compared for as tools for the classification and identification of 352 SDS-PAGE patterns of whole cell proteins of lactic acid bacteria belonging to 22 species of the genera Lactobacillus, Leuconostoc, Enterococcus, Lactococcus and Streptococcus including 47 reference strains. Electrophoretic data were pre-treated using the logistic weighting function described by Piraino et al. [Piraino, P., Ricciardi, A., Lanorte, M. T., Malkhazova, I., Parente, E., 2002. A new procedure for data reduction in electrophoretic fingerprints of whole-cell proteins. Biotechnol. Lett. 24, 1477-1482]. Hierarchical cluster analysis provided a satisfactory classification of the patterns but was unable to discriminate some species (Leuconostoc, Lb. sakei/Lb. curvatus, Lb. acidophilus/Lb. helveticus, Lb. plantarum/Lb. paraplantarum, Lc. lactis/Lc. raffinolactis). A 7x7 Kohonen self-organizing map (KSOM), trained with the patterns of the reference strains, provided a satisfactory classification of the patterns and was able to discriminate more species than hierarchical cluster analysis. The map was used in predictive mode to identify unknown strains and provided results which in 85.5% of cases matched the classification obtained by hierarchical cluster analysis. Two supervised tools, linear discriminant analysis and a 23:5:2 Bayesian network were proven to be highly effective in the discrimination of SDS-PAGE patterns of Lc. lactis from those of other species. We conclude that data reduction by logistic weighting coupled to traditional multivariate statistical analysis or artificial neural networks provide an effective tool for the classification and identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins.