Decrease In Relative Abundance Research Articles

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing.

The characterization of bacterial community compositions and the change in perfluoroalkyl acids (PFAAs) along a natural river distribution system were explored in the present study. Illumina high-throughput sequencing was used to explore bacterial community diversity and structure in sediment polluted by PFAAs from the Xiaoqing River, the area with concentrated fluorochemical facilities in China. The concentration of PFAAs was in the range of 8.44-465.60ng/g dry weight (dw) in sediment. Perfluorooctanoic acid (PFOA) was the dominant PFAA in all samples, which accounted for 94.2% of total PFAAs. High-level PFOA could lead to an obvious increase in relative abundance of Proteobacteria, ε-Proteobacteria, Thiobacillus, and Sulfurimonas and the decrease in relative abundance of other bacteria. Redundancy analysis revealed that PFOA played an important role in the formation of bacterial community, and PFOA at higher concentration could reduce the diversity of bacterial community. When the concentration of PFOA was below 100ng/g dw in sediment, no significant effect on microbial community structure was observed. Thiobacillus and Sulfurimonas were positively correlated with the concentration of PFOA, suggesting that both genera were resistant to PFOA contamination.

Spinach (Spinacia oleracea L.) modulates its proteome differentially in response to salinity, cadmium and their combination stress

Cadmium (Cd) contamination and salinity are common stressors in agricultural soils all over the globe. Sensitivity and modulation of plant proteome lead to proper signal execution and adaptation to abiotic stress via molecular responses, which strengthen plant defence system. A comparative proteomic study, employing 2DE-MALDI TOF/TOF MS, of Spinacia oleracea plants exposed to cadmium (50 μg CdCl2 g−1 soil), salinity (10 mg NaCl g−1 soil) and their combination (NaCl + Cd) was conducted to understand the minimum common adaptation to multiple stress. Analysis of 2D gel maps showed significant increase and decrease in relative abundance of 14 and 39 proteins by Cd; 11 and 46 by salinity and 22 and 37 by combined stress of Cd and salinity, respectively. Peptide mass fingerprinting (PMF) helped in the identification of maturase K and PPD4 with increased relative abundance under all stresses; whereas salinity stress and combination stress silenced the presence of one protein (polycomb protein EZ2) and two proteins (cellulose synthase-like protein and ubiquitin conjugation factor E4), respectively. The identified proteins were functionally associated with signal transduction (15%), protein synthesis (16%), stress response and defence (33%), photosynthesis (13%), plant growth/cell division (9%), energy generation (4%), transport (4%), secondary metabolism (3%), and cell death (3%); clearly indicating the importance and necessity of keeping a higher ratio of defence and disease-responsive proteins. The results suggest that plant may increase the abundance of defence proteins and may also lower the abundance of catabolic proteins. Proteins with altered ratios of abundance belonged to different functional categories, suggesting that plants have differential mechanisms to respond to Cd, salinity, and their combined stress, but with unique sets of proteins.

Abstract 4504: Plasma pharmacokinetics and tumor accumulation in mice of IMGN779, an antibody-drug conjugate for acute myeloid leukemia

Abstract IMGN779, an antibody-drug conjugate (ADC) consisting of the anti-CD33 antibody, Z4681A, linked to the potent DNA-alkylating agent, DGN462, via a charged disulfide linker, sulfo-SPDB, is in development for the treatment of acute myeloid leukemia (AML). IMGN779 is highly active in vitro against AML cell lines and primary patient AML cells and causes complete regression of AML xenograft tumors at non-toxic doses in vivo. To understand the fate of IMGN779 upon uptake, we performed metabolism studies on cultures of ADC-treated AML cells in vitro, and distribution studies in vivo, following the plasma clearance and tumor accumulation of the ADC in mice. The antigen-mediated binding, uptake, and degradation of IMGN779 by AML cells in culture were measured using a radiolabeled conjugate. CD33-targeted degradation of IMGN779 was observed in treated cultures, with metabolites detected within the cells, some as DNA-adducts, and in the media following efflux from cells. Approximately 40% of initially-bound IMGN779 was measured as protein-free degraded species after 22 h incubation at 37 °C, with an additional ∼40% measured as DNA-associated species. To evaluate plasma pharmacokinetics (PK), mice were injected with [3H]propionate radiolabeled Z4681A antibody (Ab), or with IMGN779 that was radiolabeled either on the Ab portion of the ADC ([3H]propionate) or on the DGN462 moiety. Total Ab and intact ADC concentrations were determined in plasma samples collected from 2 min to 28 days post-injection. Overlapping clearance profiles for Z4681A and Ab-labeled IMGN779 were observed with half-lives (t½) of ∼18 d, which demonstrated that conjugation with DGN462 did not alter Ab PK. A faster clearance of [3H]DGN462-labeled IMGN779 was observed, with a plasma t½ of 4.5 d, indicating that DGN462 is released from IMGN779 in circulation. Plasma samples were CD33-affinity captured and analyzed by LC/MS to determine the mass-distribution profile of IMGN779. A decrease in relative abundances of antibody species associated with a high number of DGN462 molecules from 2 min- 3 d supported the plasma clearance results. To determine the tumor localization of IMGN779 and its metabolites, the radioactivity in excised HL60/QC xenografts dosed with 5 mg/kg [3H]IMGN779 or non-targeting [3H]ADC was measured at 6, 24 and 48 h after treatment. The total amount of ADC (intact and metabolized) present was similar, but slightly higher for IMGN779 versus non-targeting ADC samples. However, the amount of both extractable metabolites and DNA-bound species was higher in tumor samples from mice treated with IMGN779 versus non-targeting ADC, indicating CD33-targeted metabolism in the tumor. From these studies, we conclude IMGN779 demonstrates CD33 target-mediated generation of DGN462 metabolites, and also exhibits DNA-modification consistent with the mechanism of action of its effector molecule, DGN462. Citation Format: Katharine C. Lai, Prerak Shah, Surina Sikka, XiuXia Sun, Rassol LaLeau, Kathleen R. Whiteman, Holly Johnson-Modafferi, Alan Wilhelm, Charlene Audette, Lintao Wang, Megan E. Bogalhas, Thomas A. Keating, Ravi Chari. Plasma pharmacokinetics and tumor accumulation in mice of IMGN779, an antibody-drug conjugate for acute myeloid leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4504. doi:10.1158/1538-7445.AM2015-4504

Proteomic analysis of early-stage embryos: implications for egg quality in hapuku (Polyprion oxygeneios)

In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function/pathway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.

Thermal evolution of aliphatic and aromatic moieties of asphaltenes from coals of different rank: possible implication to the molecular architecture of asphaltenes

The compositional and structural changes that coal asphaltenes undergo with increasing thermal maturation were investigated using solid-state 13C NMR and Fourier transform infrared spectroscopy. The results show a gradual increase in the relative proportion of carbon content with a concomitant decrease in the hydrogen, sulphur and oxygen content. The amount of aromatic carbon also increases while the aliphatic carbon decreases with increasing maturity. Ester and carboxylic groups are particularly sensitive to maturation and decrease in relative abundance with increasing maturity while the amount of aromatic carbonyl groups increases. In general, the asphaltenes were observed to evolve towards a more thermally stable structure with increasing amounts of aromatic moieties and relatively lower amounts of aliphatic moieties. The results are in agreement with the ultimate dominance of the island molecular architecture (the Yen–Mullins model) in asphaltenes.

Paleoenvironmental and paleobiological origins of coccolithophorid genusWatznaueriaemergence during the late Aalenian–early Bajocian

AbstractThe latest Aalenian–early Bajocian time interval (ca. 171-169 Ma) is marked by a global reorganization of oceanic plates with the Central Atlantic opening and the formation of the Pacific plate. This time interval is also marked by a global geochemical perturbation of δ13C with a negative excursion at the Aalenian/Bajocian boundary and a positive excursion during the early Bajocian. Evolutionary diversifications of marine invertebrate taxa, namely ammonites, radiolarians, and coccolithophorids, are recorded at that time. Concerning coccolithophorids, this interval witnesses the diversification and expansion of the most successful Mesozoic genus:Watznaueria. In this study, we explore the potential environmental, ecological, and biological forcing at the origin ofWatznaueriadiversification and its effect on the coccolith assemblages through quantification of the absolute and relative abundances of calcareous nannofossils in two Middle Jurassic key sections: Cabo Mondego (Portugal) and Chaudon-Norante (France). In both sections, we find an increase in nannofossil absolute abundance and flux at the beginning of the lower Bajocian, coeval with an increase in absolute and relative abundances ofWatznaueriaspp., followed by a plateau in the middle and upper part of the lower Bajocian. The increase ofWatznaueriaspp. is synchronous with a decrease in relative abundance of other major coccolith taxa, whereas the absolute abundance of these species did not decrease. During the climatically driven early Bajocian eutrophication event,Watznaueriaspp. integrated into the calcareous nannoplankton community in two successive evolutionary steps involving firstW. contractaandW. colaccicchii, and secondW. britannicaandW.aff.manivitiae. Step 1 was driven by an increase in niche carrying capacities linked to the early Bajocian eutrophication. Step 2 was driven by specific adaptation of the newly evolvedWatznaueriaspecies to bloom in nutrient-rich environments not exploited before. These evolutionary events have initiated the 100-Myr reign ofWatznaueriaover the calcareous nannoplankton community.

Shifting elasmobranch community assemblage at Cocos Island--an isolated marine protected area.

Fishing pressure has increased the extinction risk of many elasmobranch (shark and ray) species. Although many countries have established no-take marine reserves, a paucity of monitoring data means it is still unclear if reserves are effectively protecting these species. We examined data collected by a small group of divers over the past 21 years at one of the world's oldest marine protected areas (MPAs), Cocos Island National Park, Costa Rica. We used mixed effects models to determine trends in relative abundance, or probability of occurrence, of 12 monitored elasmobranch species while accounting for variation among observers and from abiotic factors. Eight of 12 species declined significantly over the past 2 decades. We documented decreases in relative abundance for 6 species, including the iconic scalloped hammerhead shark (Sphyrna lewini) (-45%), whitetip reef shark (Triaenodon obesus) (-77%), mobula ray (Mobula spp.) (-78%), and manta ray (Manta birostris) (-89%), and decreases in the probability of occurrence for 2 other species. Several of these species have small home ranges and should be better protected by an MPA, which underscores the notion that declines of marine megafauna will continue unabated in MPAs unless there is adequate enforcement effort to control fishing. In addition, probability of occurrence at Cocos Island of tiger (Galeocerdo cuvier), Galapagos (Carcharhinus galapagensis), blacktip (Carcharhinus limbatus), and whale (Rhincodon typus) sharks increased significantly. The effectiveness of MPAs cannot be evaluated by examining single species because population responses can vary depending on life history traits and vulnerability to fishing pressure.

Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease.

To characterize the diversity and taxonomic relative abundance of the gut microbiota in patients with never-treated, recent-onset psoriatic arthritis (PsA). High-throughput 16S ribosomal RNA pyrosequencing was utilized to compare the community composition of gut microbiota in patients with PsA (n = 16), patients with psoriasis of the skin (n = 15), and healthy, matched control subjects (n = 17). Samples were further assessed for the presence and levels of fecal and serum secretory IgA (sIgA), proinflammatory proteins, and fatty acids. The gut microbiota observed in patients with PsA and patients with skin psoriasis was less diverse when compared to that in healthy controls. This could be attributed to the reduced presence of several taxa. Samples from both patient groups showed a relative decrease in abundance of Coprococcus species, while samples from PsA patients were also characterized by a significant reduction in Akkermansia, Ruminococcus, and Pseudobutyrivibrio. Supernatants of fecal samples from PsA patients revealed an increase in sIgA levels and decrease in RANKL levels. Analysis of fatty acids revealed low fecal quantities of hexanoate and heptanoate in both patients with PsA and patients with psoriasis. Patients with PsA and patients with skin psoriasis had a lower relative abundance of multiple intestinal bacteria. Although some genera were concomitantly decreased in both conditions, PsA samples had a lower abundance of reportedly beneficial taxa. This gut microbiota profile in PsA was similar to that previously described in patients with inflammatory bowel disease and was associated with changes in specific inflammatory proteins unique to this group, and distinct from that in patients with skin psoriasis and healthy controls. Thus, the role of the gut microbiome in the continuum of psoriasis-PsA pathogenesis and the associated immune response merits further study.

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress.

Reaction of soil bacteria to drought and rewetting stress may depend on soil chemical properties. The objectives of this study were to test the reaction of different bacterial phyla to drought and rewetting stress and to assess the influence of different soil chemical properties on the reaction of soil bacteria to this kind of stress. The soil samples were taken at ten forest sites and measured for pH and the contents of organic C (Corg) and total N (Nt), Zn, Cu, and Pb. The samples were kept without water addition at 20 – 30 °C for 8 weeks and subsequently rewetted to achieve moisture equal to 50 – 60 % of their maximum water-holding capacity. Prior to the drought period and 24 h after the rewetting, the structure of soil bacterial communities was determined using pyrosequencing of 16S rRNA genes. The drought and rewetting stress altered bacterial community structure. Gram-positive bacterial phyla, Actinobacteria and Firmicutes, increased in relative proportion after the stress, whereas the Gram-negative bacteria in most cases decreased. The largest decrease in relative abundance was for Gammaproteobacteria and Bacteroidetes. For several phyla the reaction to drought and rewetting stress depended on the chemical properties of soils. Soil pH was the most important soil property influencing the reaction of a number of soil bacterial groups (including all classes of Proteobacteria, Bacteroidetes, Acidobacteria, and others) to drought and rewetting stress. For several bacterial phyla the reaction to the stress depended also on the contents of Nt and Corg in soil. The effect of heavy metal pollution was also noticeable, although weaker compared to other chemical soil properties. We conclude that soil chemical properties should be considered when assessing the effect of stressing factors on soil bacterial communities.Electronic supplementary materialThe online version of this article (doi:10.1007/s13213-014-1002-0) contains supplementary material, which is available to authorized users.

Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate.

Stillage, which is generated during bioethanol production, constitutes a promising substrate for biogas production within the scope of an integrated biorefinery concept. In this study, a microbial community was grown on thin stillage as mono-substrate in a continuous stirred tank reactor (CSTR) at a constant temperature of 55 °C, at an organic loading rate of 1.5 goTS/L*d and a retention time of 25 days. Using an amplicon-based dataset of 17,400 high-quality sequences of 16S rRNA gene fragments (V2-V3 regions), predominance of Bacteria assigned to the families Thermotogaceae and Elusimicrobiaceae was detected. Dominant members of methane-producing Euryarchaeota within the CSTR belonged to obligate acetoclastic Methanosaetaceae and hydrogenotrophic Methanobacteriaceae. In order to investigate population dynamics during reactor acidification, the organic loading rate was increased abruptly, which resulted in an elevated concentration of volatile fatty acids. Acidification led to a decrease in relative abundance of Bacteria accompanied with stable numbers of Archaea. Nevertheless, the abundance of Methanosaetaceae increased while that of Methanobacteriales decreased successively. These findings demonstrate that a profound intervention to the biogas process may result in persistent community changes and reveals uncommon bacterial families as process-relevant microorganisms.

The Early Toarcian Oceanic Anoxic Event in the External Subbetic (Southiberian Palaeomargin, Westernmost Tethys): Geochemistry, nannofossils and ichnology

The analysis of macroinvertebrates, trace fossils, calcareous nannofossils and geochemistry from Pliensbachian to Lower Toarcian deposits of the Subbetic (Southern Spain) allows us to interpret the incidence of the Toarcian Oceanic Anoxic Event (T-OAE) in the boundary between the Tethys and the Hispanic Corridor. Trace fossils from the marl-limestone rhythmite (Upper Pliensbachian to Lower Toarcian) indicate an oxygenated bottom. A dark marly interval occurs above a fossil-rich condensed surface with a negative excursion of δ18O, interpreted as evidence of the Early Toarcian transgression and a climate warming. The carbon cycle perturbation is recorded by decreasing CaCO3 content and the negative excursion of δ13C at the base of the Serpentinum Zone, NJT 6 nannofossil Zone. The barren interval for nektonic and benthic organisms at the beginning of the Serpentinum Zone confirms the oxygen restricted conditions in the sea-floor. Environmental conditions were unfavourable for the development of calcareous nannoplankton, as attested by the drop in absolute abundances. The deep photic zone seemed to be particularly hostile to phytoplankton, as shown by the decrease in relative abundance of the deep-dweller Mitrolithus jansae, related to shoaling of the oxygen minimum zone in the water column. Increasing values of redox sensitive elements and total organic carbon, as well as the record of pyrite framboids <5μm size, confirm the anoxic conditions (probably euxinic conditions in any moment) at the base of the dark marly interval (NJT 6). The return to oxic or dysoxic conditions is confirmed by the record of fossil-poor marls with scarce macroinvertebrates and microfossils, as well as the recovery of trace fossils mainly (low-oxygen tolerant Chondrites tracemakers). Increasing abundance of calcareous nannofossils and deep-dweller M. jansae indicate ameliorated environmental conditions in the water column. Geochemistry supports the recovery of carbonate production (increasing CaCO3) and oxygen availability (decrease of TOC and redox sensitive elements).

Skistodiaptomus pallidus (Copepoda: Diaptomidae) establishment in New Zealand natural lakes, and its effects on zooplankton community composition

The North American calanoid copepod Skistodiaptomus pallidus is an emerging invader globally, with non-indigenous populations recorded from constructed waters in New Zealand, Germany and Mexico since 2000. We examined the effects of S. pallidus establishment on the zooplankton community of a natural lake, Lake Kereta, where it was first recorded in late-2008, coincident with releases of domestically cultured grass carp (Ctenopharyngodon idella) . Although not present in any of our samples prior to August 2008, S. pallidus was found in all samples collected in the subsequent five years. ANOSIM indicated zooplankton community composition significantly differed between samples collected before and after S. pallidus invasion, whether the invader was included in the analysis or not. Zooplankton species affected most greatly were the copepods Calamoecia lucasi and Mesocyclops sp., which decreased in their relative importance, and the cladocerans Bosmina meridionalis and Daphnia galeata, which increased. Rotifer species were relatively unaffected. As the length of grass carp released were >6.5 cm, direct predatory effects by this species on the zooplankton community are unlikely. Associated reductions in macrophyte biomass could explain increases in the relative abundances of planktonic cladocerans (B. meridionalis and D. galeata). However, the effect of macrophyte reduction by grass carp on zooplankton communities is considered to be limited elsewhere, while the reduced macrophyte biomass cannot explain the decrease in relative abundance of the native planktonic calanoid copepod C. lucasi. Competition between C. lucasi and S. pallidus is the most compelling explanation for the reduction in importance of the native calanoid copepod species. Skistodiaptomus pallidus appears to have undergone a “boom-and-bust” cycle in Lake Kereta, increasing in relative abundance in the first three years following establishment, before declining in importance.

Effects of selective digestive decontamination (SDD) on the gut resistome

Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches. We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD. The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2″)-Ib and an aadE-like gene. We show that aph(2″)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ∼10(4) fold increase to a ∼10(-10) fold decrease in relative abundance during SDD. ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.

Effects of Stocking With Brood Fish To Management With Resident Stream Dwelling Brown Trout Salmo cf. trutta L. Stock

Management with the indigenous stock of resident brown trout Salmo cf. trutta of the Danubi-an strain in the protected area of the River Gradac with the catch-and-release fishing regime since 2000 resulted in the prime fly fishing stream in Serbia. Stocking with the brown trout parr in 2007 in the density issued by fisheries management plan supplemented with the large-sized brood fish beyond the issued fisheries measures in the upper section of the River Gradac was followed by change in structure of fish community and population structure of brown trout there. The time of maturation of brown trout was delayed and their size at maturation increased in 2008, due to the abrupt decrease in the density of their stock. That change did not affect an increase of brown trout mean weight, but only an increase of their average age, with the de-crease in relative abundance, relative biomass and annual natural production, implying the pro-longed recovery period of brown trout stock in the upper section of the River Gradac. In con-trast to that, stocking with brown trout parr only in the density issued by fisheries management plan was beneficial on the second, downstream situated section. Another prominent feature that followed stocking as a management measure was the introgression of brown trout of the Atlan-tic lineage into the gene pool of brown trout of the native, Danubian lineage, as confirmed in wild-bred brown trout.

Biostratigraphie, paléoécologie et zones d’acmé des foraminifères planctoniques au passage Crétacé-Paléogène dans la Téthys (Tunisie et Espagne) et l’Atlantique (France)

Biostratigraphical high-resolution analyses and quantitative data confirm that deposition is continuous across the K-Pg transition in several sections in Tunisia (El Kef, stratotype section) and Spain (Agost and Caravaca sections) located in the Tethyan realm and the Bidart sections in the Atlantic realm, without any relevant hiatus. The Upper Maastrichtian assemblages of planktic foraminifera from these sections are largely dominated by small biserial heterohelicids. They are associated to common species having planispiral test (i.e. globigerinelloids), trochospiral test (i.e. hedbergellids, rugoglobigerinids globotruncanids), to rare triserial heterohelicids (i.e. guembelitriids) and trochospiral species showing tubulospines (i.e. schackoinids). Stratigraphical ranges of these diverse taxa through the late Maastrichtian in the Tethyan and Atlantic realms show very few changes in the planktonic foraminiferal assemblages and most of the species are present in the Abathomphalus mayaroensis biozone. By our high-resolution sampling and the intensive research for the A. mayaroensis index species in the uppermost Maastrichtian samples, we confirm that this species is omnipresent up to the top of the Maastrichtian. Therefore, A. mayaroensis is present in almost all samples which are late Maastrichtian in age, but this species became very scarce in the uppermost Maastrichtian samples. This scarceness could be due to a climate cooling. A sharp decrease in relative abundance of the deep dwellers species, like as Abathomphalus intermedius and A. mayaroensis as well as in other keeled globotruncanids is observed at the studied sections from the Tethyan realm (indicative of low latitude) across the latest Maastrichtian. At the K/Pg boundary, all the globotruncanids disappeared. They are considered specialists living in tropical-subtropical deep seawater habitat. At this boundary, large and ornate heterohelicids also disappeared. Therefore, all the studied sections show that about 90 % of the Maastrichtian species became extinct according to a catastrophic mass extinction pattern. Only about 10 % crossed the K/Pg boundary and survived during the earliest Danian. The minor difference in the number of disappeared taxa is related to their latitude location or environment paleodepth. The changes in the species relative abundance, observed in the successive planktic foraminiferal assemblages, make it possible to recognize the Acme-stage 0 typical of the upper Maastrichtian interval. It is characterized by the highest species richness of Globotruncanids and heterohelicids specialists of tropical to subtropical marine conditions, the Acme-stage 1 typical of the Guembelitria cretacea Zone, and in particular of the Hedbergella holmdelensis Subzone dominated by “opportunists” species belonging to Guembelitria, the Acme-stage 2 which corresponds to the Pv. eugubina Zone dominated mainly by specimens belonging to Palaeoglobigerina and Parvularugoglobigerina and the Acme-stage 3 which characterizes mainly the Ps. pseudobulloides Zone dominated by biserial species belonging to Chiloguembelina and Woodringina.

Community differentiation of the cutaneous microbiota in psoriasis

BackgroundPsoriasis is a common chronic inflammatory disease of the skin. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion group), unaffected contralateral skin from psoriatic patients (unaffected group), and similar skin loci in matched healthy controls (control group) in order to discern patterns that govern skin colonization and their relationship to clinical diagnosis.ResultsUsing high-throughput 16S rRNA gene sequencing, we assayed the cutaneous bacterial communities of 51 matched triplets and characterized these samples using community data analysis techniques. Intragroup Unifrac β diversity revealed increasing diversity from control to unaffected to lesion specimens. Likewise, principal coordinates analysis (PCoA) revealed separation of the lesion samples from unaffected and control along the first axis, suggesting that psoriasis is a major contributor to the observed diversity. The taxonomic richness and evenness decreased in both lesion and unaffected communities compared to control. These differences are explained by the combined increased abundance of the four major skin-associated genera (Corynebacterium, Propionibacterium, Staphylococcus, and Streptococcus), which present a potentially useful predictor for clinical skin type. Psoriasis samples also showed significant univariate decreases in relative abundances and strong classification performance of Cupriavidus, Flavisolibacter, Methylobacterium, and Schlegelella genera versus controls. The cutaneous microbiota separated into two distinct clusters, which we call cutaneotypes: (1) Proteobacteria-associated microbiota, and (2) Firmicutes-associated and Actinobacteria-associated microbiota. Cutaneotype 2 is enriched in lesion specimens compared to control (odds ratio 3.52 (95% CI 1.44 to 8.98), P <0.01).ConclusionsOur results indicate that psoriasis induces physiological changes both at the lesion site and at the systemic level, which select for specific differential microbiota among the assayed clinical skin types. These differences in microbial community structure in psoriasis patients are potentially of pathophysiologic and diagnostic significance.

Distribution patterns of the invasive herbivore Siganus luridus (Rüppell, 1829) and its relation to native benthic communities in the central Aegean Sea, Northeastern Mediterranean

AbstractThe present study explores the distribution of the invasive herbivore fish Siganus luridus (Rüppell 1829) and its relationship to native herbivores and macroalgal assemblages in the shallow sublittoral of the Cyclades Archipelago, Aegean Sea, Greece. In situ underwater surveys of herbivore abundance (fishes and sea urchins) and algal coverage were carried out at 180 sampling sites in 18 islands. Siganus luridus accounted for 17% of the total herbivore abundance, with a decrease in relative abundance from the southeastern to the northwestern islands. In Santorini Island (in the southeast of the study area) S. luridus abundance accounted for 90% of the total herbivore fish abundance, while in Kea Island (at the northwestern limit of the study area), S. luridus was absent. The spatial variation of minimum sea surface temperature is possibly the reason for its distributional pattern. Siganus luridus abundance was found to be positively correlated to the native herbivore Sparisoma cretense (Linnaeus 1758). A significant negative relationship was found between the abundance of the invasive species and the sum of erect and canopy algae cover (Dictyotales and Cystoseira spp.), which are the main components of its diet in the region. On the other hand, its occurrence was particularly high in barren sites. The results arising from this study reinforce evidence from studies in the Eastern Mediterranean Basin that the expansion of the invasive species S. luridus may have profound impacts on native communities in the Mediterranean infralittoral zone.

Bacterial community changes along a salinity gradient in a Chinese wetland

We analyzed the composition and diversity of a bacterial community to determine its response to increasing salinity in the Xiangsi Lake wetland in the arid region of northwest China. We studied 12 sites, ranging from freshwater to saltwater habitats, using polymerase chain reaction (PCR)-based terminal restriction fragment length polymorphism (T-RFLP) and sequencing of the 16S rRNA genes of 5 selected samples. Cluster analysis and phylogenetic analysis revealed that the bacterial community changed significantly in response to increased salinity within the small-scale wetland (50.8 km(2)). Detailed analysis showed that (i) Betaproteobacteria can maintain balanced growth over a salinity range (from 0.34 to 6.86 g/L) through intergenus changes in community structure, followed by a sharp decrease in relative abundance (from 62.2% to 16.0%) when salinity reaches 26.18 g/L; (ii) salt-sensitive and halophobic taxa were progressively replaced by halotolerant and halophilic taxa with increasing salinity; (iii) bacterial diversity was lowest at intermediate salinity levels (6.86 g/L); and (iv) an increasing percentage of unclassified bacterial taxa were found with increasing salinity. This study has implications to improve understanding of bacterial community response to water salinization.

Assessing Paleo-Biodiversity Using Low Proxy Influx

We developed an algorithm to improve richness assessment based on paleoecological series, considering sample features such as their temporal resolutions or their volumes. Our new method can be applied to both high- and low-count size proxies, i.e. pollen and plant macroremain records, respectively. While pollen generally abounds in sediments, plant macroremains are generally rare, thus leading to difficulties to compute paleo-biodiversity indices. Our approach uses resampled macroremain influxes that enable the computation of the rarefaction index for the low influx records. The raw counts are resampled to a constant resolution and sample volume by interpolating initial sample ages at a constant time interval using the age∼depth model. Then, the contribution of initial counts and volume to each interpolated sample is determined by calculating a proportion matrix that is in turn used to obtain regularly spaced time series of pollen and macroremain influx. We applied this algorithm to sedimentary data from a subalpine lake situated in the European Alps. The reconstructed total floristic richness at the study site increased gradually when both pollen and macroremain records indicated a decrease in relative abundances of shrubs and an increase in trees from 11,000 to 7,000 cal BP. This points to an ecosystem change that favored trees against shrubs, whereas herb abundance remained stable. Since 6,000 cal BP, local richness decreased based on plant macroremains, while pollen-based richness was stable. The reconstructed richness and evenness are interrelated confirming the difficulty to distinguish these two aspects for the studies in paleo-biodiversity. The present study shows that low-influx bio-proxy records (here macroremains) can be used to reconstruct stand diversity and address ecological issues. These developments on macroremain and pollen records may contribute to bridge the gap between paleoecology and biodiversity studies.

Rhodobacteraceaeare the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater

The formation of biofilms and biofouling is a common feature in aquatic environments. The aim of this study was to identify the primary colonizers of biofilm formed in Eastern Mediterranean Coastal water at different seasons and follow early dynamics of biofilm community development. Pre-treated coastal seawater and biofilm samples were collected from six different sampling events of 2 weeks' duration each during 1 year. The microbial community composition and specific abundance were estimated by 16S rRNA gene clone libraries and fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM), respectively. The biofilm formed over the course of the year was fairly consistent in terms of community composition and overall abundance with the exception of spring season. Alphaproteobacteria (30-70% of total bacteria), in particular Rhodobacteraceae, were the dominant bacteria in the biofilm, regardless of season, followed by Bacteroidetes (5-35%) and Gammaproteobacteria (6-35%). There was a decrease in relative abundance of Alphaproteobacteria and an increase in the abundance of Bacteroidetes between the initial and 2-week-old biofilm. This observation may aid man-made facilities that have to deal with biofilm formation and help the development of appropriate strategies to control those biofilms.