The self-inhibited leaky integrator: Transfer functions and steady state relations

We analyse a model for neural activity including forgetting and self-inhibition processes. The analysis concerns the static and dynamic performances. The theoretical predictions are compared with previously published experimental data on the neural encoding in the ommatidia of the Limulus lateral eye. We conclude that the analysed model could reproduce the experimental behaviour, but different models cannot be excluded. Moreover an independent normalisation factor has to be assumed to account for the experimental gains.     

Pressure-induced effects on cytochrome oxidase: the aerobic steady state

If cytochrome c oxidase is subjected to pressure during the aerobic steady state, large spectral changes are apparent. These seem to be associated with the inhibition of electron transport within the oxidase. The volume change for the transition is about 80 mL/mol. When the oxidase in the aerobic steady state, with porphyrin cytochrome c (the iron-free derivative of cytochrome c) bound to it, is subjected to pressure, the porphyrin derivative is released. This results from a change in the dissociation constant of the complex. Whereas the dissociation constant during turnover is about 1.25 X 10(-8) M, during pressure-induced inhibition the dissociation constant appears to be about an order of magnitude greater. It appears as though the binding site of the inhibited, partially reduced enzyme more closely resembles that of the fully reduced enzyme than that of the enzyme during the aerobic steady state.     

Biodegradation of gaseous toluene with mixed microbial consortium in a biofilter: steady state and transient operation

Bioprocess and Biosystems Engineering - Petroleum oil refineries are massive emitters of risky volatile organic compounds (VOCs). Among the VOCs, toluene is taken into account as a significant...     

Linear and non-linear impacts of a non-native plant invasion on soil microbial community structure and function

Biological invasions can alter ecosystem functions such as litter decomposition and nutrient cycling, but little is known about how invader abundance influences the impact on the ecosystem. It is often assumed that impacts are proportional to invasion density, but this assumption has never been tested and has little justification. We tested the hypothesis that the microbial community structure and function of a mixed hardwood forest soil changed after invasion by Japanese barberry (Berberis thunbergii), an invasive shrub commonly found in eastern hardwood forests, and that changes were proportional to the density of invasion. We constructed microcosms with mixtures of native and invasive leaf litter, and measured microbial community structure (phospholipid fatty acids) and function (litter decomposition). Decomposition was linearly related to the degree of invasion (R ²?=?0.945), but the ratio of bacteria to fungi exhibited a strongly non-linear, threshold response (R ²?=?0.513). These results indicate that impacts of Japanese barberry invasion are not always proportional to invasion density. This finding has implications for the study of biological invasions as well as practical implications for the management of exotic invasive species.     

Nutritional effects of non-steady state soil salinity on a salt-tolerant wheat cultivar

Summary Biological nitrogen fixation is considered an important trait of cowpeas (Vigna unguiculata (L.) Walp. var. California Blackeye No. 5) for economical production yet the process does not alone provide the quantity of nitrogen required by the plant for maximum productivity. Two experiments were undertaken to determine the potential of an increase in nodule mass and number of bacteroids resulting in increased nitrogen fixation. Cowpeas were grown in a glasshouse for 7 weeks under conditions forcing near total dependence on biological nitrogen fixation for growth. Nodule mass on the roots was varied by inoculating seeds with various ratios of effective and ineffective rhizobia that could be identified serologically and by the color of nodule formed. The results of both experiments demonstrated a linear relationship between total nodule mass formed by the effective rhizobia and quantity of nitrogen fixed. The regression coefficients were high in both experiments (r=0.99^** and 0.91^**). The relationship between total nitrogen fixed and total number of bacteroids of the effective strain was not consistent. In one experiment the regression coefficient was 0.93^** but in the other experiment it was 0.65^**. From these results it appears that there is good potential for increasing nitrogen fixation in cowpeas by increasing nodule mass. An increase in nodule mass would also result in an increase in the number of bacteroids.     

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure,enzyme activities,and nitrogen cycling

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.     

Long-term effects of grassland management on soil microbial abundance: implications for soil carbon and nitrogen storage

Grassland management intensification can significantly affect the structure and composition of important soil microbial groups such as bacteria and fungi. Changes to these microbial communities can greatly influence carbon (C) and nitrogen (N) cycling in grassland soils. Here we specifically address how microbial abundances might shift under the effect of multiple management practices and how this in turn might relate to changes in soil C and N storage. Soil samples were collected from a 23-year-old grassland experiment and real-time quantitative Polymerase Chain Reaction (PCR) was performed to address whether and how (1) chronic nutrient additions, (2) liming (i.e., the addition of CaCO₃ to soils), and (3) grazing by rabbits might affect archaeal, bacterial and fungal microbial groups. We found that liming additions significantly increased archaeal and bacterial abundance whilst strongly reducing fungal abundance. The addition of N-only (as NH₄NO₃) significantly reduced bacterial abundance while chronic grazing by rabbits resulted in positive effects on archaeal abundance. Despite long-term grassland management significantly affecting soil microbial abundances (and Fungal-to-Bacterial ratios), microbial changes were not related to either changes in soil C or N pools. Overall, our results suggest that (1) important microbial-‘soil functioning’ relationships may only be detected at lower taxonomic levels, and (2) liming-induced increases in soil pH determined significant shifts in soil microbial abundance, which could have important consequences for the delivery of multiple soil ecosystem services (i.e., nutrient regulation, C and N sequestration) from permanent grassland.     

Use of a microbial sensor: a new approach to the measurement of inhibitory effects on the microbial activity of activated sludge

This paper presents a new method for the measurement of inhibitory effects in wastewater treatment plants on the basis of a continuous measurement of the microbial respiration product (CO(2)). The microbial sensor developed for this purpose consists of a small conical fluidized bed reactor connected to a cylindrical chamber that comprises part of the sample recirculation system. Activated sludge microbes are immobilized on spherical (diameter=1-2 mm) reticulated sinter glass carriers. Pure oxygen is supplied via the cylindrical chamber in order to sustain a highly dense population of microbial mass. The mean hydraulic retention time in the microbial sensor ranges between 30 and 40 min, while temperature is maintained at 30 degrees C, and pH 6.4. Carbon dioxide in the off-gas, which reflects the microbial activity, is continuously analyzed by means of an infrared analyzer. Inhibition of microbial activity (toxicity) can be determined as the mean percent reduction in carbon dioxide concentration. Several substances were tested and proved toxic to the microbes. With this microbial sensor, early detection of toxic substances becomes feasible, preventing them from entering an activated sludge unit operation.     

Precipitation pulse size effects on Sonoran Desert soil microbial crusts

Deserts are characterized by low productivity and substantial unvegetated space, which is often covered by soil microbial crust communities. Microbial crusts are important for nitrogen fixation, soil stabilization and water infiltration, but their role in ecosystem production is not well understood. This study addresses the following questions: what are the CO₂ exchange responses of crusts to pulses of water, does the contribution of crusts to ecosystem flux differ from the soil respiratory flux, and is this contribution pulse size dependent? Following water application to crusts and soils, CO₂ exchange was measured and respiration was partitioned through mixing model analysis of Keeling plots across treatments. Following small precipitation pulse sizes, crusts contributed 80% of soil-level CO₂ fluxes to the atmosphere. However, following a large pulse event, roots and soil microbes contributed nearly 100% of the soil-level flux. Rainfall events in southern Arizona are dominated by small pulse sizes, suggesting that crusts may frequently contribute to ecosystem production. Carbon cycle studies of arid land systems should consider crusts as important contributors because of their dynamic responses to different pulse sizes as compared to the remaining ecosystem components.     

Tobermolite effects on methane removal activity and microbial community of a lab-scale soil biocover

Three identical lab-scale biocovers were packed with an engineered soil (BC 1), tobermolite only (BC 2), and a mixture of the soil and tobermolite (BC 3), and were operated at an inlet load of 338–400 g-CH₄ m^?2 d^?1 and a space velocity of 0.12 h^?1. The methane removal capacity was 293 ± 47 g-CH₄ m^?2 d^?1 in steady state in the BC 3, which was significantly higher than those in the BC 1 and BC 2 (106 ± 24 and 114 ± 48 g-CH₄ m^?2 d^?1, respectively). Quantitative PCR indicated that bacterial and methanotrophic densities (6.62–6.78 × 10⁷ 16S rDNA gene copy number g-dry sample^?1 and 1.37–2.23 × 10⁷ pmoA gene copy number g-dry sample^?1 in the BC 1 and BC 3, respectively) were significantly higher than those in the BC 2. Ribosomal tag pyrosequencing showed that methanotrophs comprised approximately 60 % of the bacterial community in the BC 2 and BC 3, while they only comprised 43 % in the BC 1. The engineered soil favored the growth of total bacteria including methanotrophs, while the presence of tobermolite enhanced the relative abundance of methanotrophs, resulting in an improved habitat for methanotrophs as well as greater methane mitigation performance in the mixture. Moreover, a batch experiment indicated that the soil and tobermolite mixture could display a stable methane oxidation level over wide temperature (20–40 °C, at least 38 μmol g-dry sample^?1 h^?1) and pH (5–8, at least 61 μmol g-dry sample^?1 h^?1) ranges. In conclusion, the soil and tobermolite mixture is promising for methane mitigation.     

The effects of mineral fertilizer and organic manure on soil microbial community and diversity

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H ^′ ), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.     

热胁迫后施用氮肥和秸秆对土壤微生物生物量及功能的影响

研究了热胁迫(40℃,18 h)后在60 d培养期内不施物料(S)、仅施尿素(N)、仅施秸秆(R)和二者配施(RN)处理下土壤微生物生物量及土壤功能(基础呼吸、基质诱导呼吸、秸秆分解能力)的变化.结果表明:热胁迫有促进土壤微生物生物量及功能的趋势,但其影响弱且持续时间短.不论热胁迫与否,与不施物料和仅施氮肥处理相比,施用秸秆及其与氮肥配施处理下土壤微生物生物量、基础呼吸、基质诱导呼吸和秸秆分解能力均大幅提高,而单施氮肥处理与不施物料处理相比变化不明显,各项指标甚至有降低趋势.表明施用秸秆及其与氮肥配施对自然土壤和环境胁迫(干扰)后土壤功能都有改善作用.     

Root, mycorrhiza and earthworm interactions: their effects on soil structuring processes, plant and soil nutrient concentration and plant biomass

Earthworms, arbuscular mycorrhiza fungi (AMF) and roots are important components of the belowground part of terrestrial ecosystem. However, their interacting effects on soil properties and plant growth are still poorly understood. A compartmental experimental design was used in a climate chamber in order to investigate, without phosphorus (P) addition, the single and combined effects of earthworms (Allolobophora chlorotica), AMF (Glomus intraradices) and roots (Allium porrum) on soil structure, nutrient concentration and plant growth. In our experimental conditions, plant roots improved soil structure stability (at the level of macroaggregates) whereas earthworms decreased it. AMF had no effect on soil structure stability but increased P transfer from the soil to the plant and significantly increased plant biomass. Earthworms had no direct influence on P uptake or plant biomass, and the N/P ratio measured in the shoots indicated that P was limiting. Interactions between AMF and earthworms were also observed on total C and N content in the soil and on total root biomass. Their effects varied temporally and between the different soil compartments (bulk soil, rhizosphere and drilosphere). After comparison with other similar studies, we suggest that effects of earthworms and AMF on plant production may depend on the limiting factors in the soil, mainly N or P. Our experiment highlights the importance of measuring physical and chemical soil parameters when studying soil organism interactions and their influence on plant performance.     

Grass species and soil type effects on microbial biomass and activity

We evaluated plant versus soil type controls on microbial biomass and activity by comparing microbial biomass C, soil respiration, denitrification potential, potential net N mineralization and nitrification in different soils supporting four grass species, and by growing a group of 10 different grass species on the same soil, in two experiments respectively. In the first experiment, none of the microbial variables showed significant variation with grass species while all variables showed significant variation with soil type, likely due to variation in soil texture. In the second experiment, there were few significant differences in microbial biomass C among the 10 grasses but there were significant relationships between variation in microbial biomass C and potential net N mineralization (negative), soil respiration (positive) and denitrification (positive). There was no relationship between microbial biomass C and either plant yield or plant N concentration. The results suggest that 1) soil type is a more important controller of microbial biomass and activity than grass species, 2) that different grass species can create significant, but small and infrequent, differences in microbial biomass and activity in soil, and 3) that plant-induced variation in microbial biomass and activity is caused by variation in labile C input to soil.     

Protein--protein interaction maps: a lead towards cellular functions

The availability of complete genome sequences now permits the development of tools for functional biology on a proteomic scale. Several experimental approaches or in silico algorithms aim at clustering proteins into networks with biological significance. Among those, the yeast two-hybrid system is the technology of choice to detect protein-protein interactions. Recently, optimized versions were applied at a genomic scale, leading to databases on the web. However, as with any other 'genetic' assay, yeast two-hybrid assays are prone to false positives and false negatives. Here we discuss these various technologies, their general limitations and the potential advances they make possible, especially when in combination with other functional genomics or bioinformatics analyses.