Denitrifying population dynamic and evolution of nitrogen gas during a composting process

Abstract Little information exists about nitrogen losses through microbial activity during treatment of solid urban waste (SUW) by processes such as composting. In the present study, in addition to evaluating the pattern of nitrogen losses by denitrification at different stages of the process, a comparison between the method of Pochon and Tardieux, and an improved gas chromatographic method for estimating denitrifying populations was undertaken, Though the MPN (Most Probable Number) enumerations were higher using the colorimetric method than the gas chromatographic one, the patterns of the two graphs showing numbers of denitrifiers during composing were the same. The highest numbers were revealed immediately after loading the reactor (10⁷–10⁸/g d.w.), lower numbers of denitrifiers were found in the second sampling corresponding to the thermophilic phase (10³–10⁴/g d.w.). These numbers increased gradually as the waste material stabilized (10th to 123rd day of composting) to again reach values of 10⁷–10⁸/g d.w.     

Molecular characterization of fungal community dynamics in the initial stages of composting

Composting relies on a complex network of bacteria and fungi to process crude organic material. Although it is known that these organisms drive dynamic changes in temperature and pH, little is known about the temporal dynamics of fungal populations during the rise to thermophilic conditions. This study employed F-ARISA (fungal-automated rRNA intergenic spacer analysis) and 18S rRNA gene cloning and sequencing to examine changes in community structure during this period. Sequencing of the 18S rRNA portion of cloned F-ARISA products revealed the presence of four distinct fungal genera including Backusella sp., Mucoraceae, Geotrichum sp. and the yeast Pichia sp. Based on the presence and absence of these ARISA operational taxonomic units (A-OTUs), we observed a shift in fungal community structure between 48 and 60 h. This change in community structure preceded a rise in pH and coincided with an increase in temperature. Clone libraries constructed using fungi-specific 18S rRNA primers contained sequences similar to several other fungal genera including Penicillium sp., Aspergillus sp., Hamigera sp., Neurospora sp. and the yeast Candida sp. While the fungal species richness was relatively low at any time point, the community structure was dynamic and paralleled changes in bacterial community structure.     

Factors affecting the population dynamics of Suaeda maritima at initial stages of development

This study describes life history and population dynamics of the annual halophyte Suaeda maritima, at initial stages of seedling development, in salt-marshes of the Mont-Saint-Michel Bay. Effects of salinity on seed germination and seedling development were studied both in the laboratory and in the field. Salinity was measured as sediment electrical conductivity. Experiments in the laboratory showed that Suaeda maritima was relatively tolerant to salinity during the germination stage. In the field, germination occurred when soil salinity was minimal. Almost all seeds germinated in the field; this may explain the absence of a persistent seed bank. Salinity did not seem to affect the growth of seedlings either. Mortality in the field was attributed to physical factors such as anoxia during temporary immersion, burial by sediment and tidal uprooting. The intensity of these effects varied according to the location of Suaeda maritima seedlings: in hollows, along the edge of tidal creeks, in gaps among dense vegetation cover, or in pattern with Puccinellia maritima. Perennial vegetation did not restrict Suaeda maritima germination. In contrast, perennials such as Puccinellia maritima and Halimione portulacoides limited the development of Suaeda maritima seedlings since only a small number of this annual emerged beneath their canopies. The fate of seedlings depended to a great extent on the permeability of the perennial canopy to light. Thus, disturbance resulting in bare patches inside the perennial vegetation seemed essential for the development of this annual species. Suaeda maritima can grow in the presence of Puccinellia maritima so long as the latter present as an open matrix. Suaeda maritima may also benefit from protection against desiccation and tidal action where this occurs.     

Analysis of the microbial community structure in a membrane bioreactor during initial stages of filtration

Membrane biofouling was investigated during the early stages of filtration in a laboratory-scale membrane bioreactor operated on molasses wastewater. The bacterial diversity and composition of the membrane biofilm and activated sludge were analyzed using terminal restriction fragment length polymorphism coupled with 16S rRNA clone library construction and sequencing. The amount of extracellular polymeric substances produced by bacteria was investigated using spectroscopic methods. The results reveal that the bacterial community of activated sludge differs significantly from that of the membrane biofilm, especially at the initial phase. Phylogenetic analysis based on 16S rRNA gene sequences identified 25 pioneer OTUs responsible for membrane surface colonization. Also, the relationship between the identified bacterial strains and the system specifications was explored.     

Methodological aspects of microcalorimetry used to assess the dynamics of microbial activity during composting

Isothermal microcalorimetry is a sensitive non-invasive analytical tool that can become useful in research on compost and other biosolids. The aim of the present study was to address several methodological aspects that are critical to the use of microcalorimetry to assess the dynamics of microbial activity in such systems. The results show that: (1) The calorimetric baseline is strongly influenced by the run temperature in the range relevant to composting systems (20–60 °C), and is also affected by addition of the water that is required to maintain or optimize microbial activity, presumably because some water evaporates through ampoule gaskets. (2) Amending mature compost with readily available substrates requires additional careful baseline treatment. (3) Sample heterogeneity can be successfully minimized by passing through a 2-mm sieve. Additional size separation can be useful to enable focusing on the more active fractions. (4) Oxygen depletion is a key feature in batch calorimetric analysis; for samples of highly active composts or manure, the total amount of heat released relative to the oxygen available in the ampoule may indicate the co-existence of anaerobic and aerobic metabolic pathways. Finally, practical recommendations for microcalorimetry analyses of pre-mature and mature composts are outlined.     

Use of the systems approach in modeling the growth dynamics of a microbial biomass taking into account the cell division process]

The possibility of using systemic approach in the construction of the mathematical model allowing for changes in the biomass and the number of cells is shown. Definite rules were followed in the process of construction, calculations were made with the use of a computer. The satisfactory coincidence of rated and experimental data was achieved (in this instance, E. coli M17 were used).     

Insight into the binding mode of a novel LSD1 inhibitor by molecular docking and molecular dynamics simulations

Abstract

Lysine-specific demethylase (LSD1) is an important enzyme for histone lysine methylation. Downregulated LSD1 expression has been linked to cancer proliferation, migration and invasion, indicating that it is an important target for anti-cancer medication. In the present study, the binding modes of a recent reported new series of LSD1 inhibitor were analyzed by using molecular docking and molecular dynamics simulations. A binding mode of these inhibitors was proposed based on the results. According to this binding mode, Thr628 can form two important hydrogen bonds with these inhibitors. Moreover, if the inhibitors can form an additional hydrogen bond with hydroxyl group of Ser289, the potency of the inhibitor can be greatly improved, such as the best inhibitor (compound 12d) in this series. Hydrophobic interactions between the inhibitors and LSD1 are also key contributor here, such as the interaction between the hydrophobic groups (benzene rings) of the inhibitors and the hydrophobic residues of LSD1 (including Val288, Val317, Val811, Ala814, Leu659, Trp751 and Tyr761). Based on the results and analysis, it may provide some useful information for future novel LSD1 inhibitor design.     

Mathematical modeling of the population dynamics of a distinct interactions type system with local dispersal

Distinct biotic interactions in multi-species communities are a ubiquitous force in the natural ecosystem, and this force is an essential determinant of community stability and species coexistence outcomes. We conduct numerical simulations and bifurcation analysis of partial differential equations to gain better understanding and ecological insights into how predation (a), predator handling time (h), and local dispersal affect multi-species community dynamics. This system consists of resource-mutualist-exploiter-competitor interactions and local dispersal. From the inspection of our numerical simulations and co-dimension one bifurcation analysis findings, we discover several critical values that correspond to transcritical bifurcation, subcritical and supercritical Hopf bifurcations. This occurs as we vary the bifurcation parameters a and h in this complex ecological system under symmetric and asymmetric dispersal scenarios. Furthermore, the interplay between these local bifurcation points results in an exciting co-dimension two bifurcations, i.e., Bogdanov-Takens and cusp bifurcation points, respectively, which act as the synchronization points in this complex ecological system. From an ecological viewpoint, we find that (i) the effect of the no-dispersal scenario supports the maintenance of species biodiversity when the predation strength is moderate; (ii) symmetric dispersal induces both subcritical and supercritical Hopf bifurcation and support species diversity for moderate predation strength; and (iii) asymmetric dispersal promotes species diversity as it simplifies the bifurcation changes in dynamics by eliminating the subcritical bifurcations that trigger uncertainty, and this dispersal mechanism mediates species coexistence outcomes. Fundamentally, stable limit cycles have been reported as predator handling time varies in some ecological models; however, we observed in our bifurcation analysis the emergence of the unstable limit cycle as predator handling time changes. We discover that intense predator handling time destabilizes this complex ecological community. In general, our results demonstrate the influential roles of predation, predator handling time, and local dispersal in determining this system’s coexistence dynamics. This knowledge provides a better understanding of species conservation and biological control management.     

A simple model of plankton population dynamics coupled with a LES of the surface mixed layer

The concentration of phytoplankton in the sea is affected by biological processes, such as growth/mortality rates, predatory zooplankton concentrations and nutrient levels. Phytoplankton concentrations are also influenced by physical processes, in particular the mixing properties of the local fluid environment. On planktonic scales (approximately 10-1000 microm) one can assume the local turbulent flow is isotropic, with no distinction between horizontal and vertical mixing. However, agglomerations of phytoplankton into patches are observed on larger scales of up to hundreds of metres, whose formation will be influenced by the anisotropic advection/mixing properties and large-eddy structures prevalent in the surface mixed layer. This paper presents the results of the coupling of a large-eddy simulation (LES) model of the mixed layer with an advection-diffusion system of coupled equations for nitrate-phytoplankton-zooplankton (NPZ) concentration, incorporating sub-grid parameterizations of the biological processes. Typically these include phytoplankton growth due to light levels and ambient nitrate concentration, offset by grazing losses due to the presence of zooplankton. The primary goal of this work is to investigate how the characteristics of the mixed layer turbulence influence the observed distribution of phytoplankton. One novel feature is the incorporation of a 'vortex-force' term in the LES code in order to generate Langmuir circulations. It has been speculated that the enhanced mixing rates associated with 'Langmuir turbulence' play a significant role in regulating planktonic activity. Results derived from the coupled LES-NPZ model, run with and without the presence of Langmuir circulations, are presented in order to investigate these ideas.     

Comparison of the microbial population dynamics and phylogenetic characterization of a CANOXIS reactor and a UASB reactor degrading trichloroethene

AIMS: To understand the microbial ecology underlying trichloethene (TCE) degradation in a coupled anaerobic/aerobic single stage (CANOXIS) reactor oxygenated with hydrogen peroxide (H2O2) and in an upflow anaerobic sludge bed (UASB) reactor. METHODS AND RESULTS: The molecular study of the microbial population dynamics and a phylogenetic characterization were conducted using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). In both reactors, TCE had a toxic effect on two uncultured bacterial populations whereas oxygen favoured the growth of aerobic species belonging to Rhizobiaceae and Dechloromonas. No methanotrophic bacteria were detected when targeting 16S rRNA gene with universal primers. Alternatively, pmo gene encoding the particulate methane monooxygenase of Methylomonas sp. LW21 could be detected in the coupled reactor when H2O2 was supplied at 0.7 g O2 l day(-1). CONCLUSIONS: Methylomonas sp. LW21 that could be responsible for the aerobic degradation of the TCE by-products is not among the predominant bacterial populations in the coupled reactor. It seems to have been outcompeted by heterotrophic bacteria (Rhizobiaceae and Dechloromonas sp.) for oxygen. SIGNIFICANCE AND IMPACT OF THE STUDY: The results obtained show the limitations of the coupled reactor examined in this study. Further investigations should focus on the operating conditions of this reactor in order to favour the growth of the methanotrophs.     

The role of mixotrophic protists in the population dynamics of the microbial food web in a small artificial pond

• 1 The seasonal variations of protist and rotifer populations were monitored over 1 year in a small artificial pond. Grazing rates on fluorescently labelled bacteria were also determined.
• 2 The data showed population dynamics similar to other small freshwater bodies; diatoms were numerous during the spring, chlorophytes dominated during the summer months, and mixotrophs, in particular Gymnodinium, dominated during the autumn and winter.
• 3 The mixotrophic dinoflagellates were responsible for a high chlorophyll concentration during the autumn and winter. Mixotrophs were important consumers of bacteria, particularly during the autumn when population densities of pure heterotrophs were low. Mixotrophs were an important component of the microbial food web in this pond.

     

The role of local ecology during hybridization at the initial stages of ecological speciation in a marine snail

Hybrid zones of ecologically divergent populations are ideal systems to study the interaction between natural selection and gene flow during the initial stages of speciation. Here, we perform an amplified fragment length polymorphism (AFLP) genome scan in parallel hybrid zones between divergent ecotypes of the marine snail Littorina saxatilis, which is considered a model case for the study of ecological speciation. Ridged‐Banded (RB) and Smooth‐Unbanded (SU) ecotypes are adapted to different shore levels and microhabitats, although they present a sympatric distribution at the mid‐shore where they meet and mate (partially assortatively). We used shell morphology, outlier and nonoutlier AFLP loci from RB, SU and hybrid specimens captured in sympatry to determine the level of phenotypic and genetic introgression. We found different levels of introgression at parallel hybrid zones and nonoutlier loci showed more gene flow with greater phenotypic introgression. These results were independent from the phylogeography of the studied populations, but not from the local ecological conditions. Genetic variation at outlier loci was highly correlated with phenotypic variation. In addition, we used the relationship between genetic and phenotypic variation to estimate the heritability of morphological traits and to identify potential Quantitative Trait Loci to be confirmed in future crosses. These results suggest that ecology (exogenous selection) plays an important role in this hybrid zone. Thus, ecologically based divergent natural selection is responsible, simultaneously, for both ecotype divergence and hybridization. On the other hand, genetic introgression occurs only at neutral loci (nonoutliers). In the future, genome‐wide studies and controlled crosses would give more valuable information about this process of speciation in the face of gene flow.     

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO₂-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin–Benson–Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO₂-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.     

Introduction of the European minnow into a subalpine lake: habitat use and long-term changes in population dynamics

Minnows Phoxinus phoxinus , studied 30 years after the first record of the species in the subalpine Lake Øvre Heimdalsvatn, Norway, ≥55 mm L _T, were estimated to have densities of c . 4.7 kg ha⁻¹ (120 000 fish) in June 1999 and 2.1 kg ha⁻¹ (63 000 fish) in June 2000. The population was characterized by low individual growth, delayed age of maturity and lived longer when compared to values reported in a previous study in the early phase of its establishment, and other values reported in the literature. Most minnows reached sexual maturity at 4–5 years and >55 mm L _T. Although the estimated annual survival of minnows >55 mm was low ( S =0.2), ages up to 13 years were recorded. Despite a moderate increase in the population size during the last 20 years, the present reduction in individual growth, followed by delayed age of maturity, suggested the existence of density-dependent effects on the population dynamics of the minnows. The minnows were restricted to the littoral zone and near bottom areas. A vertical or horizontal expansion in habitat use was probably prevented by the presence of piscivorous brown trout Salmo trutta .     

Reconstituting initial events during the assembly of apolipoprotein B-containing lipoproteins in a cell-free system

The synthesis of apolipoprotein B (apoB) dictates the formation of chylomicrons and very low-density lipoproteins, two major lipoprotein precursors in the human plasma. Despite its biological significance, the mechanism of the assembly of these apoB-containing lipoproteins remains elusive. An essential obstacle is the lack of systems that allow fine dissection of key components during assembly, including nascent apoB peptide, lipids in defined forms, chaperones, and microsomal triglyceride transfer protein (MTP). In this study, we used a prokaryotic cell-free expression system to reconstitute early events in the assembly of apoB-containing lipoprotein that involve the N-terminal domains of apoB. Our study shows that N-terminal domains larger than 20.5% of apoB (B20.5) have an intrinsic ability to remodel vesicular phospholipid bilayers into discrete protein-lipid complexes. The presence of appropriate lipid substrates during apoB translation plays a pivotal role for successful lipid recruitment, and similar lipid recruitment fails to occur if the lipids are added posttranslationally. Cotranslational presence of MTP can dramatically promote the folding of B6.4-20.5 and B6.4-22. Furthermore, apoB translated in the presence of MTP retains its phospholipid recruitment capability posttranslationally. Our data suggest that during the synthesis of apoB, the N-terminal domain has a short window for intrinsic phospholipid recruitment, the time frame of which is predetermined by the environment where apoB synthesis occurs. The presence of MTP prolongs this window of time by acting as a chaperone. The absence of either proper lipid substrate or MTP may result in the improper folding of apoB and, consequently, its degradation.     

毛竹种群向针阔林扩张的根系形态可塑性

为了弄清毛竹(Phyllostachys edulis)向针阔林扩张过程中根系的形态可塑性反应,在浙江天目山自然保护区毛竹向针阔林扩张的典型过渡地带,连续区域上设置毛竹纯林、针阔-毛竹混交林(以下简称过渡林)、针阔林3种样地。用根钻法采集样地毛竹根系、针阔树根系并比对其生物量密度、细根比根长、相邻同级侧根节点距等形态特征参数变化。结果表明:随着毛竹的扩张程度增加,林内根系生物量密度增加;且与针阔树竞争过程中毛竹将更多的根系放置于表层;同时在水平方向上随离样株距离的增加未出现明显变化,而针阔树根系则随离样木距离的增加而逐渐减少;毛竹根系比根长明显增加,平均增幅15%;一、二级侧根节点距则均有所下降,毛竹侧根数量增多。这些结果表明毛竹种群可通过根系生物量密度、细根比根长、相邻同级侧根节点距等形态可塑性方式实现向周边森林扩张。     

Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling,molecular dynamics simulation,binding free energy prediction and density functional theory calculation

Abstract

The mitochondrial calcium uniporter (MCU) is the critical protein of the inner mitochondrial membrane that is the primary mediator for calcium uptake into the mitochondrial matrix. Herein we built the optimal homology model of human MCU which was refined through all-atom molecular dynamics simulation. Then, the binding mode of known inhibitor was predicted through molecular docking method, along with molecular dynamics simulation and binding free energy calculation to verify the docking result and stability of the protein-inhibitor complex. Finally, density functional theory (DFT) calculation enhanced our understanding of the molecular interaction of MCU inhibitor. Our research would provide a deeper insight into the interactions between human MCU and its inhibitor, which boosts to develop novel therapy against MCU related disease.

Communicated by Ramaswamy H. Sarma