Nutrient-rich Environment Research Articles

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine.

BackgroundThe microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.MethodsThe genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.ResultsWe present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.DiscussionThis revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.

The presence of biofilm forming microorganisms on hydrotherapy equipment and facilities.

Hydrotherapy equipment provides a perfect environment for the formation and growth of microbial biofilms. Biofilms may reduce the microbiological cleanliness of hydrotherapy equipment and harbour opportunistic pathogens and pathogenic bacteria. The aims of this study were to investigate the ability of microorganisms that colonize hydrotherapy equipment to form biofilms, and to assess the influence of temperature and nutrients on the rate of biofilm formation. Surface swab samples were collected from the whirlpool baths, inhalation equipment and submerged surfaces of a brine pool at the spa center in Ciechocinek, Poland. We isolated and identified microorganisms from the swab samples and measured their ability to form biofilms. Biofilm formation was observed at a range of temperatures, in both nutrient-deficient and nutrient-rich environments. We isolated and identified microorganisms which are known to form biofilms on medical devices (e.g. Stenotrophomonas maltophilia). All isolates were classified as opportunistic pathogens, which can cause infections in humans with weakened immunity systems. All isolates showed the ability to form biofilms in the laboratory conditions. The potential for biofilm formation was higher in the presence of added nutrients. In addition, the hydrolytic activity of the biofilm was connected with the presence of nutrients.

Ecological Stoichiometry of Ocean Plankton.

Marine plankton elemental stoichiometric ratios can deviate from the Redfield ratio (106C:16N:1P); here, we examine physiological and biogeochemical mechanisms that lead to the observed variation across lineages, regions, and seasons. Many models of ecological stoichiometry blend together acclimative and adaptive responses to environmental conditions. These two pathways can have unique molecular mechanisms and stoichiometric outcomes, and we attempt to disentangle the two processes. We find that interactions between environmental conditions and cellular growth are key to understanding stoichiometric regulation, but the growth rates of most marine plankton populations are poorly constrained. We propose that specific physiological mechanisms have a strong impact on plankton and community stoichiometry in nutrient-rich environments, whereas biogeochemical interactions are important for the stoichiometry of the oligotrophic gyres. Finally, we outline key areas with missing information that is needed to advance understanding of the present and future ecological stoichiometry of ocean plankton.

Evaluating the chronic effects of nitrate on the health and performance of post-smolt Atlantic salmon Salmo salar in freshwater recirculation aquaculture systems

Commercial production of Atlantic salmon smolts, post-smolts, and market-size fish using land-based recirculation aquaculture systems (RAS) is expanding. RAS generally provide a nutrient-rich environment in which nitrate accumulates as an end-product of nitrification. An 8-month study was conducted to compare the long-term effects of “high” (99±1mg/L NO3-N) versus “low” nitrate-nitrogen (10.0±0.3mg/L NO3-N) on the health and performance of post-smolt Atlantic salmon cultured in replicate freshwater RAS. Equal numbers of salmon with an initial mean weight of 102±1g were stocked into six 9.5m3 RAS. Three RAS were maintained with high NO3-N via continuous dosing of sodium nitrate and three RAS were maintained with low NO3-N resulting solely from nitrification. An average daily water exchange rate equivalent to 60% of the system volume limited the accumulation of water quality parameters other than nitrate. Atlantic salmon performance metrics (e.g. weight, length, condition factor, thermal growth coefficient, and feed conversion ratio) were not affected by 100mg/L NO3-N and cumulative survival was >99% for both treatments. No important differences were noted between treatments for whole blood gas, plasma chemistry, tissue histopathology, or fin quality parameters suggesting that fish health was unaffected by nitrate concentration. Abnormal swimming behaviors indicative of stress or reduced welfare were not observed. This research suggests that nitrate-nitrogen concentrations≤100mg/L do not affect post-smolt Atlantic salmon health or performance under the described conditions.

Holocene history of landscape development in the catchment of Lake Skogstjern, southeastern Norway, based on a high-resolution multi-proxy record

A high-resolution multi-proxy record from sediments of a small-sized lake situated in Telemark, southeastern Norway, was used to reconstruct the local landscape development of the past c. 10,500 years. Our data demonstrate that changes in vegetation composition and structure in the first two-thirds of the Holocene are principally attributable to climatic changes and high erosion rates, as deduced from geochemical and physical (loss-on-ignition) proxy analyses. The highest signals of erosional inputs to the lake (c. 8030–5760 cal. BP) can be correlated with the first part of the Holocene Thermal Maximum. Nevertheless, evidence from pollen, non-pollen palynomorphs and microscopic charcoal analyses indicates the presence of nutrient-rich and disturbed environments already during the middle Mesolithic (c. 10,050–9400 cal. BP). It also shows traces of animal husbandry (c. 5580 cal. BP) and small-scale cereal cultivation (c. 5520 cal. BP) in the early Neolithic. In subsequent periods, human impact remains at a relatively low level and does not generate significant palaeo-environmental changes. Not until the second half of the Bronze Age (c. 2840 cal. BP) is some intensification in animal husbandry recorded, whereas crop cultivation continues to play a minor role in the second millennium BP. The establishment of a full farming economy took place during the Roman Iron Age (c. 1790 cal. BP), characterised by extensive forest clearance and local fires, crop cultivation in permanent fields and the presence of open pastures. This establishment is associated with advanced soil degeneration and increased erosion rates.

A Gerecse pannóniai puhatestűi és lelőhelyeik: rétegtan, őskörnyezet és fejlődéstörténet

A Gerecse földtani térképezése során a Magyar Földtani és Geofizikai Intézet geológusai új, vagy régen feledésbe merült és részletesen soha nem dokumentált pannóniai feltárásokat azonosítottak a hegység északi előterében, az onnan dél felé felnyúló völgyekben, és a hegység belsejében is. Az ezekből begyűjtött puhatestű fauna (kiegészítve a már korábban ismert tatai puhatestű faunával és régebbi gyűjteményi anyagokkal) és a feltárásokban megfigyelhető szedimentológiai jellemzők alapján a pannóniai rétegsor itt is, mint az egész Dunántúli-középhegység északnyugati peremén, egyetlen transzgresszív-regresszív ciklusból áll. A ciklus transzgresszív szárnyát a tatai téglagyári feltárásokban a vékony transzgresszív bázisrétegre települő Száki Formáció kékesszürke agyagja és az abban megőrződött mély szublitorális fauna, míg a Gerecse központi részén, a tardosi Vályus-kút környékén, 375 méter tengerszint feletti magasságban a lignites agyaggal kezdődő rétegsor fedőjében települő, szintén mély szublitorális puhatestűeket tartalmazó agyag képviseli. A dunaszentmiklósi Iván halála-völgyben valószínűleg egy szökőár hozta létre a kréta fekü anyagából képződött konglomerátumot, homokos mátrixában tömegesen megjelenő zárt (két teknős) pannóniai kagylóhéjakkal. Az üledékciklus regresszív szárnyát az Újfalui Formáció képződményei adják; ezek legjobb feltárásai a Gerecse északi előterében, a Neszmély környéki völgyekben (Nyáraska-völgy, Disznós-kúti-völgy, Csekendi-völgy) és Süttő környékén találhatók. A formációt felépítő felfelé sekélyedő, néhány méter vastag ciklusok faunája a kagylók uralta sekély szublitorális együttesekből, a csigák magas diverzitásával jellemzett litorális faunákból és végül mocsári puhatestű együttesekből áll. Gyűjteményi anyagokban előfordulnak folyóvízi fajok is. A transzgresszív szárny a Congeria czjzeki zóna felső részébe tartozik, míg a regresszív szárny a Lymnocardium ponticum zóna része; a teljes ciklus képződésének kora 9,4–8,7 millió év lehetett. A fáciesek elterjedése alapján a transzgresszió már tagolt térszínen játszódott le, majd az üledékképződéssel egyidejűleg is folyt a terület vetődéses deformációja, de a tatai és vályus-kúti rétegsorok közötti nagy magasságbeli különbség csak további vetőmozgásokkal, a Gerecse utólagos kiemelkedése nyomán jöhetett létre.

Bacteriophage\u2013prokaryote dynamics and interaction within anaerobic digestion processes across time and space

BackgroundBacteriophage–prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage–host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells.ResultsEquipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P < 0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed phage–prokaryote pairs were shallowly conserved since they were detected only within small viral clades.ConclusionsThose results collectively demonstrate phages as a major biotic factor in controlling prokaryotic composition and process performance. Therefore, phages may play a larger role in shaping prokaryotic community dynamics and process performance of anaerobic digesters than currently appreciated.

Effects of nutrients and zooplankton on the phytoplankton community structure in Marudu Bay

Current study was carried out to provide a better understanding on spatial and temporal variations in the phytoplankton community structure in Marudu Bay, an important nursery ground for fishery resources within the Tun Mustapha Marine Park and Coral Triangle Initiative, and their relationship with environmental variables. Samplings were conducted monthly from April 2014 to April 2015 in Marudu Bay, Malaysia. Water samples were collected for nutrients analysis, zooplankton and phytoplankton counting. Moreover, the in situ environmental parameters were also examined. The field study showed a total of forty seven phytoplankton genera, representative of 33 families were identified. The nutrient concentrations in Marudu Bay was low (mesotrophic) throughout the year, where the phytoplankton community was often dominated by Chaetoceros spp. and Bacteriastrum spp. In general, increase in nitrate concentration triggered the bloom of centric diatom, Chaetoceros spp. and Bacteriastrum spp. in Marudu Bay. However, the bloom of these phytoplankton taxa did not occur in the presence of high ammonia concentration. In addition, high abundance of zooplankton also a limiting factor of the phytoplankton blooms particularly at end of southwest monsoon. High silica concentration promoted the growth of pennate diatoms, Proboscia spp. and Thallassionema spp., but the depletion of silica quickly terminated the bloom. Interestingly, our study showed that Chaetoceros spp., tolerated silica depletion condition, but the average cell size of this taxon reduced significantly. In summary, the phytoplankton community structure in mesotrophic environment is more sensitive to the changes in zooplankton abundance, nutrient concentration and its ratio than that in nutrient rich environments. This study also recommends that bivalve farming at industrial scale is not recommended in Marudu Bay because it potentially depletes the primary productivity hence jeopardizing the availability of live food for larvae of many natural fishery resources in the bay.

Nitrogen budget in integrated aquaculture systems with Nile tilapia and Amazon River prawn

The present work aims to describe the nitrogen (N) budget in integrated aquaculture systems with Nile tilapia (Oreochromis niloticus) and Amazon River prawn (Macrobrachium amazonicum) in earthen ponds, with and without the addition of different substrates. The experimental design was completely randomized, with three treatments (without a substrate, with a geotextile fabric substrate, and with a bamboo substrate) and four replications. Diet was the major input of N in the systems, ranging from ~65 to 71% and followed by inlet water (~26–31%). The portion retained in reared animals and periphyton ranged from ~21 to 25% (being ~21–24% in fish and prawns). The outputs that contributed most to the accumulation and release of N were, respectively, sediment (~24–38%) and N2 (~30–36%) emitted to the atmosphere. The addition of substrates did not improve the accumulation of nitrogen in the biomass of the target species. This suggests that the periphyton had a minor role on feed availability. In general, the systems were not efficient in using nitrogen since only ~22% of all available nitrogen was retained into prawn and tilapia biomass. On the other hand, the emission of N2 (an inert gas) to the atmosphere almost compensated the nitrogen supplied in the diet that was not assimilated by the reared animals and periphyton. In addition, data suggest that the integrated aquaculture in stagnant ponds may sequester substantial amounts of nitrogen from nutrient-rich aquatic environments and could be used as a mitigation tool.

Abstract P6-02-01: Metabolic stress induces GD2 expression and cancer stem cell phenotype in triple negative breast cancer

Abstract Breast cancer stem cells (BCSCs) have been characterized as a fraction of cells in primary tumors that are drug resistant and have metastatic potential. Ganglioside GD2 has been shown by us and others as a marker for BCSCs. Furthermore, nutrient deprivation associated metabolic stress seen during tumor progression is reportedly associated with the cancer stem cell phenotype. We hypothesized that metabolic stress could induce spontaneous generation of GD2+ BCSCs during tumor progression. To test our hypothesis, we cultured breast cancer cell lines MDA-MB-231 and SUM159 at low seeding density and measured percentage and absolute number of GD2+ cells daily. Flow cytometry analysis revealed that the percentage of GD2+ cells increased from 4.5 ± 2.5 on day 2 to 15 ± 3.8% on day 5 in MDA MB-231 cells and from 8.5 ± 2.8% on day2 to 28 ± 6.2% on day 5 in SUM159 cells (both designated as triple-negative breast cancer, TNBC). To investigate this phenomenon in-vivo, we injected GFP+ MDA-MB-231 cells in NSG mice mammary fat pads and examined GD2 expression in the implanted tumors weekly. Interestingly, we noticed that the percentage of GD2+ also increased from 12 ± 1.5% on week 1 to 30 ± 2.5% on week 6. Next, SUM159 cells were cultured in either nutrient rich (NR, i.e., 10% serum) or nutrient deprived (ND, 1% serum) for 4 days. We found that the percentage of GD2+ cells in NR medium at the end of 4 day culture was ~20% of the total cell population, whereas in ND medium was almost 50%. We then tested the effects of nutrient rich environment on GD2 expression by refreshing the media daily. Interestingly, cells that received fresh media had lower number of GD2+ cells (15 ± 1.5%) compared to cells cultured in the same medium for 4 days (33 ± 2.5%). Our data suggests that nutrient deprivation induces a stem cell phenotype in TNBC cells. Next, we performed global metabolic profiling (i.e., for a total of 300 biochemical metabolites) using a mass spectroscopy-based approach. We profiled SUM159 cells cultured with NR vs. ND medium (set-1); GD2+ vs GD2- SUM159 cells (set -2); GD2+ vs GD2- MDA-MB-231 cell (set-3). Metabolites associated with amino acid metabolism, in particular glutathione metabolism, including glutamyl-alanine, 5-oxy-proline, proline, glutamine, and glutathione itself were found to be most highly up-regulated in GD2+ compared to GD2- cells and also in cells cultured in serum starved compared to serum rich conditions. Further analysis of these metabolites and their association with GD2+ cell signature raveled that gamma-glutamyl transferase (GGT5), was one of the most highly up-regulated (&amp;gt;150-fold) gene across all the groups. GGT is expressed on cell surface and transfers glutamyl group to amino acids, which then get transported across the membrane. In cancer, cells expressing GGT has been shown to be resistant to chemotherapeutic agents including cisplatin. Targeting glutathione metabolism could be future therapeutic strategy to inhibit BCSC growth in TNBC. Citation Format: Battula VL, Piyaranthna B, Nguyen K, Sun JC, Jin F, Coarfa C, Nagireddy P, Andreeff M. Metabolic stress induces GD2 expression and cancer stem cell phenotype in triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-02-01.

Interactive Effects Between Reindeer and Habitat Fertility Drive Soil Nutrient Availabilities in Arctic Tundra

Herbivores impact nutrient availability and cycling, and the net effect of herbivory on soil nutrients is generally assumed to be positive in nutrient-rich environments and negative in nutrient-poor ones. This is, however, far from a uniform pattern, and there is a recognized need to investigate any interactive effects of herbivory and habitat fertility (i.e., plant C/N ratios) on soil nutrient availabilities. We determined long-term effects of reindeer on soil extractable nitrogen (N) and phosphorus (P) and their net mineralization rates along a fertility gradient of plant carbon (C) to N and P ratios in arctic tundra. Our results showed that reindeer had a positive effect on soil N in the more nutrient-poor sites and a negative effect on soil P in the more nutrient-rich sites, which contrasts from the general consensus. The increase in N availability was linked to a decrease in plant and litter C/N ratios, suggesting that a shift in vegetation composition toward more graminoids favors higher N cycling. Soil P availability was not as closely linked to the vegetation and is likely regulated more by herbivore-induced changes in soil physical and chemical properties. The changes in soil extractable N and P resulted in higher soil N/P ratios, suggesting that reindeer could drive the vegetation toward P-limitation. This research highlights the importance of including both the elements N and P and conducting studies along environmental gradients in order to better understand the interactive effects of herbivory and habitat fertility on nutrient cycling and primary production.

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses.

Pollution from nutrients in aquatic habitats has been linked to increases in disease vectors, including mosquitoes and other pestiferous insects. One possibility is that changes in mosquito microbiomes are impacted by nutrient enrichments and that these changes affect various traits, including larval development, susceptibility to larval control agents, and susceptibility of the adult mosquitoes to pathogens. We tested this hypothesis using field mesocosms supplemented with low- and high-organic-nutrient regimens and then sampled microbial communities associated with the naturally colonizing Culex nigripalpus mosquito vector. By high-throughput sequencing of 16S rRNA gene sequences, we found no significant differences in overall microbial communities associated with sampled mosquitoes, despite detecting discernible differences in environmental variables, including pH, dissolved oxygen, and nutrient amendments. Nevertheless, indicator species analysis revealed that members of the Clostridiales were significantly associated with mosquitoes that originated from high-nutrient enrichments. In contrast, members of the Burkholderiales were associated with mosquitoes from the low-nutrient enrichment. High bacterial variability associated with the life stages of the C.nigripalpus was largely unaffected by levels of nutrient enrichments that impacted larval microbial resources, including bacteria, ciliates, and flagellates in the larval environments. IMPORTANCE Mosquito microbiota provide important physiological and ecological attributes to mosquitoes, including an impact on their susceptibility to pathogens, fitness, and sensitivity to mosquito control agents. Culex nigripalpus mosquito populations transmit various pathogens, including the Saint Louis and West Nile viruses, and proliferate in nutrient-rich environments, such as in wastewater treatment wetlands. Our study examined whether increases in nutrients within larval mosquito developmental habitats impact microbial communities associated with C.nigripalpus mosquitoes. We characterized the effects of organic enrichments on microbiomes associated with C.nigripalpus mosquitoes and identified potential bacterial microbiota that will be further investigated for whether they alter mosquito life history traits and for their potential role in the development of microbial-based control strategies.

Bacterial Networks on Hydrophobic Micropillars.

Bacteria have evolved as intelligent microorganisms that can colonize and form highly structured and cooperative multicellular communities with sophisticated singular and collective behaviors. The initial stages of colony formation and intercellular communication are particularly important to understand and depend highly on the spatial organization of cells. Controlling the distribution and growth of bacterial cells at the nanoscale is, therefore, of great interest in understanding the mechanisms of cell-cell communication at the initial stages of colony formation. Staphyloccocus aureus, a ubiquitous human pathogen, is of specific clinical importance due to the rise of antibiotic resistant strains of this species, which can cause life-threatening infections. Although several methods have attempted to pattern bacterial cells onto solid surfaces at single cell resolution, no study has truly controlled the 3D architectures of growing colonies. Herein, we present a simple, low-cost method to pattern S. aureus bacterial colonies and control the architecture of their growth. Using the wetting properties of micropatterened poly(dimethyl siloxane) platforms, with help from the physiological activities of the S. aureus cells, we fabricated connected networks of bacterial microcolonies of various sizes. Unlike conventional heterogeneous growth of biofilms on surfaces, the patterned S. aureus microcolonies in this work grow radially from nanostrings of a few bacterial cells, to form micrometer-thick rods when provided with a nutrient rich environment. This simple, efficient, and low-cost method can be used as a platform for studies of cell-cell communication phenomena, such as quorum sensing, horizontal gene transfer, and metabolic cross-feeding especially during initial stages of colony formation.

Effects of Bacillus Serine Proteases on the Bacterial Biofilms.

Serratia marcescens is an emerging opportunistic pathogen responsible for many hospital-acquired infections including catheter-associated bacteremia and urinary tract and respiratory tract infections. Biofilm formation is one of the mechanisms employed by S. marcescens to increase its virulence and pathogenicity. Here, we have investigated the main steps of the biofilm formation by S. marcescens SR 41-8000. It was found that the biofilm growth is stimulated by the nutrient-rich environment. The time-course experiments showed that S. marcescens cells adhere to the surface of the catheter and start to produce extracellular polymeric substances (EPS) within the first 2 days of growth. After 7 days, S. marcescens biofilms maturate and consist of bacterial cells embedded in a self-produced matrix of hydrated EPS. In this study, the effect of Bacillus pumilus 3-19 proteolytic enzymes on the structure of 7-day-old S. marcescens biofilms was examined. Using quantitative methods and scanning electron microscopy for the detection of biofilm, we demonstrated a high efficacy of subtilisin-like protease and glutamyl endopeptidase in biofilm removal. Enzymatic treatment resulted in the degradation of the EPS components and significant eradication of the biofilms.

Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions.

Microbes associate with animal hosts, often providing shelter in a nutrient-rich environment. The gut, however, can be a harsh environment with members of the microbiome settling in distinct niches resulting in more stable, adherent biofilms. These diverse communities can provide orders of magnitude more gene products than the host genome; selection and maintenance of a functionally relevant and useful microbiome is now recognized to be an essential component of homeostasis. Germ-free (GF) model systems allow dissection of host-microbe interactions in a simple and direct way where each member of the symbiosis can be studied in isolation. In addition, because immune defenses in the gut are often naïve in GF animals, host immune recognition and responses during the process of colonization can be studied. Ciona intestinalis, a basal chordate, is a well-characterized developmental model system and holds promise for addressing some of these important questions. With transparent juveniles, Ciona can be exposed to distinct bacterial isolates by inoculating GF artificial seawater; concentrated bacteria can subsequently be visualized in vivo if fluorescent stains are utilized. Rearing GF Ciona is a first step in untangling the complex dialogue between bacteria and innate immunity during colonization.

Macroinvertebrate fauna and depositional environment of the lower Upper Cenomanian Oberhäslich Formation in the Saxonian Cretaceous Basin (Germany)

In Saxony (southeast Germany), the global early Late Cretaceous transgression is reflected by the onlap of shallow-marine siliciclastics of the lower Upper Cenomanian Oberhäslich Formation (Calycoceras naviculare Zone) onto the eastern Erzgebirge, the central part of the emergent Mid-European Island. Based on detailed logging of sections south of Dresden and the study of extensive collection material, the depositional environment and macroinvertebrate assemblages of the Oberhäslich Formation have been reconstructed. This unit, with a mean thickness of 10–15m, usually shows a fining-upward trend that may become reversed towards the top, was laid down in a single 3rd-order sea-level cycle and is capped by an unconformity at the base of the overlying upper Upper Cenomanian Dölzschen Formation (sequence boundary Cenomanian 5; junction of the Calycoceras naviculare and Metoicoceras geslinianum zones). The macroinvertebrate assemblage of the Oberhäslich Formation, collected mainly from bioturbated, fine- or rarely medium-grained, quartz-rich sandstones, is fairly diverse, comprising nearly 50 taxa, predominantly bivalves (94.3%). Most conspicuous and abundant are relatively large forms such as Rhynchostreon (R.) suborbiculatum (25%) and Inoceramus pictus spp. (21%), eponymous taxa of the Rhynchostreon suborbiculatum/Inoceramus pictus assemblage. Non-bivalve benthic invertebrates are rare and represented by rather poorly preserved irregular and regular echinoids, siliceous sponges, a few gastropods, crustacean remains and a single starfish. Common Thalassinoides and Ophiomorpha burrows indicate that crustaceans were an important part of the infauna. Pervasive bioturbation resulted in a post-depositional homogenization of the sediments while all body fossils are preserved as (composite) internal moulds. The guild structure of the Rhynchostreon suborbiculatum/Inoceramus pictus assemblage shows a predominance of epifaunal and semi-infaunal suspension feeders (95.3%), suggesting eutrophic and unstable “green-water conditions” of an inner-shelf setting. Deposit-feeding biota are rare. The common occurrence of articulated bivalves and storm-induced shell beds indicate episodic rapid burial, most probably by tempestites. A current-influenced, well-oxygenated and nutrient-rich environment slightly below fair-weather base is inferred for the fine-grained sandy, fossiliferous sediments of the Oberhäslich Formation.

Viewing the effects of species loss in complex ecological networks

Species loss is becoming a major threat to ecosystems. An urgent task in ecology is to predict the consequence of species loss which requires an extending of our traditional study of the topology of network structure to the population dynamic analyses in complex food webs. Here, via numerical simulations of the model combining structural networks with nonlinear bioenergetic models of population dynamics, we analyzed the secondary effects of species removal on biomass distribution and population stability, as well as the factors influencing these effects. We found that the biomass of target species, the nutrient supply, and the trophic level of target species were the three most significant determiners for the effects of species loss. Species loss had large negative effect on the biomass of the species with small biomass or intermediate trophic levels, especially in infertile environment. The population stability of the species with large biomass or low trophic level is easily to be influenced especially in nutrient-rich environment. Our findings indicate the species which are easily to be affected by species loss in food webs, which may help ecologists to outline a better conservation policy.

Grazer impacts on algal community structure vary with the coastal upwelling regime

Community dynamics are often influenced by processes operating at large spatial scales. For example, the structure and dynamics of rocky intertidal communities depend not only on local factors, but also on the nearshore oceanic processes that affect the delivery of nutrients, propagules, and food particles. Conceptual models such as the grazer-reversal hypothesis predict that grazers will decrease the diversity of primary producers in nutrient-poor environments and increase diversity in nutrient-rich environments. To test this hypothesis, natural variation in the productivity of nearshore waters around the south island of New Zealand was used as a backdrop against which the occurrence of limpets, the dominant grazers, was experimentally manipulated. Limpets were either excluded or allowed access to replicate plots at five sites, two of relatively high nutrient availability and three of relatively low nutrient availability. Limpets had a negative effect on algal species richness and biomass at the nutrient-poor sites and little effect at the nutrient-rich sites, thus supporting the predictions of the grazer-reversal hypothesis. Results from this experiment suggest that in contrast to earlier results in the low zone, in the high zone of the rocky intertidal stronger bottom up effects (higher nutrients) did not “flow” up the food chain (to the herbivore level) to produce stronger top down effects. This finding is consistent with the idea that increasing environmental stress can alter the strength and direction of species interactions expected under a top-down/bottom-up scenario.

Hyperglycaemia and Pseudomonas aeruginosa acidify cystic fibrosis airway surface liquid by elevating epithelial monocarboxylate transporter 2 dependent lactate-H+ secretion.

The cystic fibrosis (CF) airway surface liquid (ASL) provides a nutrient rich environment for bacterial growth including elevated glucose, which together with defective bacterial killing due to aberrant HCO3− transport and acidic ASL, make the CF airways susceptible to colonisation by respiratory pathogens such as Pseudomonas aeruginosa. Approximately half of adults with CF have CF related diabetes (CFRD) and this is associated with increased respiratory decline. CF ASL contains elevated lactate concentrations and hyperglycaemia can also increase ASL lactate. We show that primary human bronchial epithelial (HBE) cells secrete lactate into ASL, which is elevated in hyperglycaemia. This leads to ASL acidification in CFHBE, which could only be mimicked in non-CF HBE following HCO3− removal. Hyperglycaemia-induced changes in ASL lactate and pH were exacerbated by the presence of P. aeruginosa and were attenuated by inhibition of monocarboxylate lactate-H+ co-transporters (MCTs) with AR-C155858. We conclude that hyperglycaemia and P. aeruginosa induce a metabolic shift which increases lactate generation and efflux into ASL via epithelial MCT2 transporters. Normal airways compensate for MCT-driven H+ secretion by secreting HCO3−, a process which is dysfunctional in CF airway epithelium leading to ASL acidification and that these processes may contribute to worsening respiratory disease in CFRD.

Comparative genomics of Paracoccus sp. SM22M-07 isolated from coral mucus: insights into bacteria-host interactions.

One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.