Nutrient-rich Environment Research Articles

Lactoylglutathione lyase, a critical enzyme in methylglyoxal detoxification, contributes to survival of Salmonella in the nutrient rich environment

Glyoxalase I which is synonymously known as lactoylglutathione lyase is a critical enzyme in methylglyoxal (MG) detoxification. We assessed the STM3117 encoded lactoylglutathione lyase (Lgl) of Salmonella Typhimurium, which is known to function as a virulence factor, due in part to its ability to detoxify methylglyoxal. We found that STM3117 encoded Lgl isomerises the hemithioacetal adduct of MG and glutathione (GSH) into S-lactoylglutathione. Lgl was observed to be an outer membrane bound protein with maximum expression at the exponential growth phase. The deletion mutant of S. Typhimurium (Δlgl) exhibited a notable growth inhibition coupled with oxidative DNA damage and membrane disruptions, in accordance with the growth arrest phenomenon associated with typical glyoxalase I deletion. However, growth in glucose minimal medium did not result in any inhibition. Endogenous expression of recombinant Lgl in serovar Typhi led to an increased resistance and growth in presence of external MG. Being a metalloprotein, Lgl was found to get activated maximally by Co2+ ion followed by Ni2+, while Zn2+ did not activate the enzyme and this could be attributed to the geometry of the particular protein-metal complex attained in the catalytically active state. Our results offer an insight on the pivotal role of the virulence associated and horizontally acquired STM3117 gene in non-typhoidal serovars with direct correlation of its activity in lending survival advantage to Salmonella spp.

Paleoenvironmental analyses of surface sediments from the Bohai Sea, China, using diatoms and silicoflagellates

Diatom and silicoflagellate fossils from surface sediments were analyzed at 63 sites in the Bohai Sea. Their spatial variations of the fossils were indicative of past environmental conditions, hydrodynamics, and the interaction of the Yellow Sea intrusion and Yellow River discharge into the Bohai Sea. In total, 162 taxa were identified. Higher species diversity and lower abundance occurred near the mouth of the Yellow River and Laizhou Bay, while lower species diversity and higher abundance occurred in the Central Bohai Sea and Bohai Strait. The spatial differences between fossil diversity and abundance are strongly related to the freshwater and sediment inputs from the Yellow River; lower salinity provides a diverse habitat for brackish and marine species, while a higher deposition rate can dilute the fossil concentrations. Three distinct biofacies representing the Laizhou Bay, Central Bohai Sea and Bohai Strait were classified after principal component analysis. The dominant species along the salinity gradient shifted from Paralia sulcata in the Bohai Strait to Cyclotella stylorum and Dictyocha messanensis in the Laizhou Bay, while a mixing zone existed in the Central Bohai Sea. The canonical correspondence analysis between major species and environmental factors indicated a relationship between P. sulcata and the Yellow Sea intrusion, with significant positive correlations being observed between salinity gradient, water depth and autumn temperature. In comparison, C. stylorum and D. messanensis were related to the discharge of the Yellow River, having significant positive correlations with the low-salinity and nutrient-rich environment. (C) 2014 Elsevier B.V. All rights reserved.

Extracellular excystation and development of Cryptosporidium: tracing the fate of oocysts within Pseudomonas aquatic biofilm systems.

BackgroundAquatic biofilms often serve as environmental reservoirs for microorganisms and provide them with a nutrient-rich growth environment under harsh conditions. With regard to Cryptosporidium, biofilms can serve as environmental reservoirs for oocysts, but may also support the growth of additional Cryptosporidium stages.ResultsHere we used confocal laser scanning microscopy, scanning electron microscopy (SEM), and flow cytometry to identify and describe various Cryptosporidium developmental stages present within aquatic biofilm systems, and to directly compare these to stages produced in cell culture. We also show that Cryptosporidium has the ability to form a parasitophorous vacuole independently, in a host-free biofilm environment, potentially allowing them to complete an extracellular life cycle. Correlative data from confocal and SEM imaging of the same cells confirmed that the observed developmental stages (including trophozoites, meronts, and merozoites) were Cryptosporidium. These microscopy observations were further supported by flow cytometric analyses, where excysted oocyst populations were detected in 1, 3 and 6 day-old Cryptosporidium-exposed biofilms, but not in biofilm-free controls.ConclusionsThese observations not only highlight the risk that aquatic biofilms pose in regards to Cryptosporidium outbreaks from water distribution systems, but further indicate that even simple biofilms are able to stimulate oocyst excystation and support the extracellular multiplication and development of Cryptosporidium within aquatic environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0281-8) contains supplementary material, which is available to authorized users.

Glucose and palmitate uncouple AMPK from autophagy in human aortic endothelial cells.

Dysregulated autophagy and decreased AMP-activated protein kinase (AMPK) activity are each associated with atherogenesis. Atherogenesis is preceded by high circulating concentrations of glucose and fatty acids, yet the mechanism by which these nutrients regulate autophagy in human aortic endothelial cells (HAECs) is not known. Furthermore, whereas AMPK is recognized as an activator of autophagy in cells with few nutrients, its effects on autophagy in nutrient-rich HAECs has not been investigated. We maintained and passaged primary HAECs in media containing 25 mM glucose and incubated them subsequently with 0.4 mM palmitate. These conditions impaired basal autophagy and rendered HAECs more susceptible to apoptosis and adhesion of monocytes, outcomes attenuated by the autophagy activator rapamycin. Glucose and palmitate diminished AMPK activity and phosphorylation of the uncoordinated-51-like kinase 1 (ULK1) at Ser555, an autophagy-activating site targeted by AMPK. 5-Aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR)-mediated activation of AMPK phosphorylated acetyl-CoA carboxylase, but treatment with AICAR or other AMPK activators (A769662, phenformin) did not restore ULK1 phosphorylation or autophagosome formation. To determine whether palmitate-induced ceramide accumulation contributed to this finding, we overexpressed a ceramide-metabolizing enzyme, acid ceramidase. The increase in acid ceramidase expression ameliorated the effects of excess nutrients on ULK1 phosphorylation, without altering the effects of the AMPK activators. Thus, unlike low nutrient conditions, AMPK becomes uncoupled from autophagy in HAECs in a nutrient-rich environment, such as that found in patients with increased cardiovascular risk. These findings suggest that combinations of AMPK-independent and AMPK-dependent therapies may be more effective alternatives than either therapy alone for treating nutrient-induced cellular dysfunction.

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22 Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X. bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X. bisporus. However, transcriptomes at optimal (∼ 0.89) versus low aw (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X. bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a 'chaophile', preferring solutes that disorder biomolecular structures. Both X. bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of 'chaophiles'.

Abstract SY44-03: Targeting the unfolded protein response in cancer

Abstract SY44-03: Targeting the unfolded protein response in cancer

Regime shifts between free-floating plants and phytoplankton: a review

Field studies evidence shifts between phytoplankton and free-floating plant regimes; yet, it is unclear what drives these shifts and if they are critical transitions (alternative stable states). In this review, we synthesized field and experimental data on free-floating plants (of varying size and phylogenies) and phytoplankton regimes, to assess the effects of these producers on the environment. Nutrient-rich environments promote free-floating plants domi- nance—regardless of life form—which causes dark and anoxic environments, and nutrient release from sediments. This reinforces free-floating plants domi- nance, but controls phytoplankton biomass by strong shading (despite high nutrients and low grazing). Phytoplankton dominance renders turbid and oxygen- rich (when producing) environments. We also searched for case studies of regime shifts for free- floating plants and phytoplankton dominance. Most studies showed that when free-floating plants domi- nance was interrupted, phytoplankton biomass (usu- ally Cyanobacteria) rose steeply. Likewise, when phytoplankton-dominated, the development of dense mats of free-floating plants covers usually controlled phytoplankton. Field evidence that suggests critical transitions include abrupt regime transitions in time and space; yet, evidence including indoor controlled experiments and mathematical models is needed for conclusive evidence of alternative stable states to be drawn.

How Many Initiator tRNA Genes Does Escherichia coli Need?

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNAi) genes, encoding a special tRNA (tRNA(fMet)) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between E. coli strains that differ in the number of tRNAi genes they contain. This has enabled us to uncover an unexpected link between the number of tRNAi genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNAi genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNAi gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.

Use of macrophytes in the bioassessment of the health of King’wal Wetland, Lake Victoria Basin, Kenya

King’wal wetland, at the upper catchment of Lake Victoria, is undergoing anthropogenic disturbances which degrade its health. In this study, the wetland's health was assessed using water quality parameters and wetland macrophytes, sampled monthly at five stations from November 2010 to February 2011, and the health was evaluated using the Plant Index of Biotic Integrity. Mean dissolved oxygen and biological oxygen demand were significantly different among the stations (F = 10.67, p = 0.000 and F = 10.12, p = 0.000, respectively). Correlation matrix in principle component analysis for stations and the two mean measurements were negative in stations 3, 4 and 5 with component 1 at 62.3% variance and component 2 at 33.9% variance, and positive for mean TN and TP in the same stations indicating a nutrient rich environment. Anthropogenic activities including agriculture, livestock grazing, human settlement and urbanization were the main threats to the health of King’wal wetland. The index scores at the three transect delineated areas with minimum disturbance (ST 3) and those that were highly disturbed (ST 5). However, the entire wetland can be classified as being moderate in health. Wise use and regular monitoring of the wetland is recommended to ensure maintenance of its health.

A Shrimp C-type Lectin Inhibits Proliferation of the Hemolymph Microbiota by Maintaining the Expression of Antimicrobial Peptides

Some aquatic invertebrates such as shrimp contain low albeit stable numbers of bacteria in the circulating hemolymph. The proliferation of this hemolymph microbiota in such a nutrient-rich environment is tightly controlled in healthy animals, but the mechanisms responsible had remained elusive. In the present study, we report a C-type lectin (MjHeCL) from the kuruma shrimp (Marsupenaeus japonicus) that participates in restraining the hemolymph microbiota. Although the expression of MjHeCL did not seem to be modulated by bacterial challenge, the down-regulation of its expression by RNA interference led to proliferation of the hemolymph microbiota, ultimately resulting in shrimp death. This phenotype was rescued by the injection of recombinant MjHeCL, which restored the healthy status of the knockdown shrimp. A mechanistic analysis revealed that MjHeCL inhibited bacterial proliferation by modulating the expression of antimicrobial peptides. The key function of MjHeCL in the shrimp immune homeostasis might be related to its broader recognition spectrum of the hemolymph microbiota components than other lectins. Our study demonstrates the role of MjHeCL in maintaining the healthy status of shrimp and provides new insight into the biological significance of C-type lectins, a diversified and abundant lectin family in invertebrate species.

Antimicrobial defense systems in saliva.

The oral cavity is one of the most heavily colonized parts of our body. The warm, nutrient-rich and moist environment promotes the growth of a diverse microflora. One of the factors responsible for the ecological equilibrium in the mouth is saliva, which in several ways affects the colonization and growth of bacteria. In this paper, we discuss the various mechanisms by which the composition of the oral microflora is modulated by saliva. Saliva covers the oral hard and soft tissues with a conditioning film which governs the initial attachment of microorganisms, a crucial step in the setup of the oral microflora. It furthermore contains proteins which in the soluble phase bind to bacteria, blocking their adherence to surfaces. When the supply of nutrients is diminished, bacteria use salivary glycoproteins, especially high-molecular-weight mucins, as a source of complex carbohydrates, requiring a consortium of microorganisms for breakdown. In this way saliva promotes the complexity of the oral microflora, which in itself protects against overgrowth by few pathogenic species. Finally, saliva harbors a large panel of antimicrobial proteins which directly and indirectly inhibit uncontrolled outgrowth of bacteria. These include lactoferrin, lactoperoxidase, lysozyme and antimicrobial peptides. Under pathological conditions serum leakage occurs, and saliva mobilizes the humoral and cellular defense mechanisms in the blood. In sum, saliva favors the establishment of a highly diverse microflora, rather than a semisterile environment.

Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex

BackgroundWithin the genus Streptococcus, only Streptococcus thermophilus is used as a starter culture in food fermentations. Streptococcus macedonicus though, which belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is also frequently isolated from fermented foods mainly of dairy origin. Members of the SBSEC have been implicated in human endocarditis and colon cancer. Here we compare the genome sequence of the dairy isolate S. macedonicus ACA-DC 198 to the other SBSEC genomes in order to assess in silico its potential adaptation to milk and its pathogenicity status.ResultsDespite the fact that the SBSEC species were found tightly related based on whole genome phylogeny of streptococci, two distinct patterns of evolution were identified among them. Streptococcus macedonicus, Streptococcus infantarius CJ18 and Streptococcus pasteurianus ATCC 43144 seem to have undergone reductive evolution resulting in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to Streptococcus gallolyticus subsp. gallolyticus. In addition, the three species seem to have lost genes for catabolizing complex plant carbohydrates and for detoxifying toxic substances previously linked to the ability of S. gallolyticus to survive in the rumen. Analysis of the S. macedonicus genome revealed features that could support adaptation to milk, including an extra gene cluster for lactose and galactose metabolism, a proteolytic system for casein hydrolysis, auxotrophy for several vitamins, an increased ability to resist bacteriophages and horizontal gene transfer events with the dairy Lactococcus lactis and S. thermophilus as potential donors. In addition, S. macedonicus lacks several pathogenicity-related genes found in S. gallolyticus. For example, S. macedonicus has retained only one (i.e. the pil3) of the three pilus gene clusters which may mediate the binding of S. gallolyticus to the extracellular matrix. Unexpectedly, similar findings were obtained not only for the dairy S. infantarius CJ18, but also for the blood isolate S. pasteurianus ATCC 43144.ConclusionsOur whole genome analyses suggest traits of adaptation of S. macedonicus to the nutrient-rich dairy environment. During this process the bacterium gained genes presumably important for this new ecological niche. Finally, S. macedonicus carries a reduced number of putative SBSEC virulence factors, which suggests a diminished pathogenic potential.

Chapter Ten - Epigenetic Modifications Underlying Symbiont–Host Interactions

The development, existence, and functioning of numerous animals and plants depend on their symbiotic interactions with other organisms, mainly microorganisms. In return, the symbionts benefit from safe habitats and nutrient-rich environments provided by their hosts. In these interactions, genetic changes in either of the partners may provide fitness advantages and become subjects to natural selection. Recent findings suggest that epigenetic changes, heritable or within the organism's life time, in either of the partners play significant roles in the establishment of symbiotic relationships. In this review, a variety of epigenetic effects underlying the most common host-symbiont interactions will be examined to determine to what extent these effects are shared in various interactions and how the epigenetic pathways could possibly be manipulated to benefit the interacting symbionts.

The Bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is Reduced by Flavodoxin and Ferredoxin and Is Essential under Mixotrophic, Nitrate-limiting Conditions

Cyanobacteria are able to use solar energy for the production of hydrogen. It is generally accepted that cyanobacterial NiFe-hydrogenases are reduced by NAD(P)H. This is in conflict with thermodynamic considerations, as the midpoint potentials of NAD(P)H do not suffice to support the measured hydrogen production under physiological conditions. We show that flavodoxin and ferredoxin directly reduce the bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 in vitro. A merodiploid ferredoxin-NADP reductase mutant produced correspondingly more photohydrogen. We furthermore found that the hydrogenase receives its electrons via pyruvate:flavodoxin/ferredoxin oxidoreductase (PFOR)-flavodoxin/ferredoxin under fermentative conditions, enabling the cells to gain ATP. These results strongly support that the bidirectional NiFe-hydrogenases in cyanobacteria function as electron sinks for low potential electrons from photosystem I and as a redox balancing device under fermentative conditions. However, the selective advantage of this enzyme is not known. No strong phenotype of mutants lacking the hydrogenase has been found. Because bidirectional hydrogenases are widespread in aquatic nutrient-rich environments that are capable of triggering phytoplankton blooms, we mimicked those conditions by growing cells in the presence of increased amounts of dissolved organic carbon and dissolved organic nitrogen. Under these conditions the hydrogenase was found to be essential. As these conditions close the two most important sinks for reduced flavodoxin/ferredoxin (CO2-fixation and nitrate reduction), this discovery further substantiates the connection between flavodoxin/ferredoxin and the NiFe-hydrogenase.

Genome Diversity of Spore-Forming Firmicutes.

Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.

Optimization and control in bacterial Lag phase

The lag phase of bacterial growth is important from a medical and food safety perspective, but difficult to study due to the low density and metabolic rate of cells. A new study by Alon and colleagues reveals that the gene expression program during early lag phase prioritizes carbon source utilization enzymes over genes responsible for biomass accumulation. This cellular strategy ultimately maximizes growth, making the best long-term use of the new nutrient-rich environment.See research article: http://www.biomedcentral.com/1752-0509/7/136

Palaeoecology and palaeogeography of Late Ordovician (Katian–Hirnantian) cephalopods of the Boda Limestone, Siljan district, Sweden

The carbonates associated with the Late Ordovician (Katian–Hirnantian) Boda mounds of the Siljan district, Sweden, contain a rich cephalopod fauna. Cephalopods are rare in the micritic stromatactis facies of the Katian Boda Core Member, but are concentrated together with other molluscs and trilobites in synsedimentary fillings of caves and crevices of the lithified mound limestone. More than 60 cephalopod species are known from these fillings. The assemblage is dominated in richness and abundance by small orthoconic proteoceratids of the genus Isorthoceras and by curved barrandeocerids, and is considerably less endemic than the benthic fauna of the Boda mounds. Similarities are remarkable at the species level with assemblages from elsewhere in Baltica, with Avalonia and south-western Kazakhstan. A genus-level comparison reveals affinities with Laurentia. However, the genus-level similarities are interpreted as reflecting mainly similarities of the depositional environment and of physicochemical conditions. The presence of calcareous algae in the Boda Limestone and maximum hydrostatic septal strength of cephalopods indicate a depositional depth of <100 m, well within the euphotic zone. The dominance and diversity of cephalopods with vertical migrant lifestyle and the absence of actinocerids indicate a cool, nutrient-rich deeper neritic environment. The post-Katian sediments contain a drastically reduced diversity, dominated by orthocerids. The maximum hydrostatic septal strength of the Hirnantian cephalopods and sedimentological features indicate a shallowing during the Hirnantian, but a continuation of high food availability for cephalopods in the water column.

Production characteristics of N2O during stabilization of municipal solid waste in an intermittent aerated semi-aerobic bioreactor landfill

An intermittent aerated semi-aerobic bioreactor landfill has the advantages such as accelerating stabilization of municipal solid waste (MSW), reducing methane, and in situ nitrogen removal. However, the introduction of air into a nutrient rich environment induces nitrification and denitrification processes, as well as the potential to generate N species at intermediate oxidation states, including nitrous oxide (N2O). In this study, a simulated intermittent aerated semi-aerobic bioreactor landfill was designed and operated for 262d in order to establish the production characteristics of N2O. The N2O concentration changed significantly with the degree of MSW stabilization, a low concentration level ranged from undetectable to 100ppm in the initial stabilization period, then one or two orders of magnitude higher in the later stabilization period compared with the initial period. It is clear that N2O production is relevant to the biodegradable organics in leachate and refuse. Once the biodegradable carbon sources were insufficient, which limited the activity of denitrifying organisms, higher N2O production began.

Termite mounds may not be foraging hotspots for mega-herbivores in a nutrient-rich matrix

Abstract:Our study investigated the influence of termitaria on vegetation utilization by elephants in Chewore North, Zimbabwe. Ten termite mounds and ten similar sized control plots were surveyed for soil nutrients, tree species diversity and plant biomass removal by elephants. Termite mounds had higher mean (± SE) concentrations of P, Ca, Mg and Na (0.15 ± 0.01, 48.8 ± 9.32, 5.78 ± 1.59 and 0.47 ± 0.12 meq per 100 g respectively) than control plots (0.05 ± 0.01, 3.33 ± 0.56, 1.53 ± 0.22 and 0.19 ± 0.02 meq per 100 g). However, Shannon Wiener index of tree diversity did not vary significantly between termite mounds (1.13 ± 0.280) and their control plots (0.827 ± 0.469). Contrary to most studies investigating patterns of vegetation utilization by large mammalian herbivores on termitaria, biomass removal was five times more on control plots than termite mounds. No difference in biomass removal was noted for Colophospermum mopane which had enough replicates for statistical analysis both on termite mounds and control plots. Our study negates the hypothesis that nutrient-rich soil patches will act as feeding hotspots for large mammalian herbivores. We concluded that vegetation utilization by elephants may be tree species specific, particularly in nutrient-rich environments.

Metagenomic Sequencing of Prokaryotic Microbiota from Tropical Surface Seawater

Tropical seawater harbors a rich diversity of microorganisms as a result of its nutrient-rich environment, constant supply of sufficient sunlight, and warm climate. In this report, we present the complexity of the microbial diversity of the surface seawater of the Georgetown coast as determined using next-generation sequencing technology.