Sample records for abundant coastal clade

  1. Using the urtA Gene to Profile Nitrogen Stress Adaptation and Spatio-Temporal Abundance of Synechococcus Clades in the California Current System

    NASA Astrophysics Data System (ADS)

    Chatterjee, T.; Shilova, I. N.; Zehr, J. P.

    2015-12-01

    Among the planet's most abundant photosynthetic groups, the picocyanobacteria Synechococcus contributes nearly a quarter of our global oxygen supply. Urea, from both natural and anthropogenic sources, is an important alternative to the preferred yet limited sources of reduced nitrogen for cyanobacteria in the marine environment. While urea uptake activity has been observed during nitrogen (N) limitation, this stress adaptation is not well-studied in natural habitats. We propose the urtAgene, which encodes the substrate-binding subunit of the urea-uptake ABC transporter, as a molecular marker to profile cell abundance and stress response in relation to N fluctuation. Strains prevalent in temperate waters of the California Current System - Synechococcus CC9311 (clade I), CC9605 (clade II) and CC9902/BL107 (clade IV) - were targeted by clade-specific qPCR assays to measure urtA gene copy abundance in samples from different geographical stations and a time-series. Spatial and seasonal patterns in clade abundance resembled those previously reported by studies using other Synechococcus marker genes, thus validating urtA as a strong marker. Synechococcus clades I and IV were most abundant in coastal and transitional stations, while the more oligotrophic clade II was detected near open waters. Synechococcus abundances were highest before and after the annual upwelling season, as supported by a non clade-specific rbcL-qPCR assay. A lack of correlation between abundance and nitrate availability indicated utilization of alternative nitrogen sources like urea, which was further evidenced by the detection of clade IV urtA transcripts at the station closest to shore. Urea concentrations tend to be highest in coastal environments due to fertilizer runoff, which can stimulate phytoplankton blooms including harmful algal blooms. This study adds to insight on how such environmental factors are related to N-cycling and patterns of urea-assimilating microbial populations like

  2. Spatial Abundance, Diversity, and Activity of Ammonia-Oxidizing Bacteria in Coastal Sediments of the Liaohe Estuary.

    PubMed

    Chang, Yongkai; Fan, Jingfeng; Su, Jie; Ming, Hongxia; Zhao, Wen; Shi, Yan; Ji, Fengyun; Guo, Limei; Zan, Shuaijun; Li, Bochao; Guo, Hao; Guan, Daoming

    2017-05-01

    Ammonia-oxidizing bacteria (AOB) play an important role in nitrification in estuaries. The aim of this study was to examine the spatial abundance, diversity, and activity of AOB in coastal sediments of the Liaohe Estuary using quantitative PCR, high-throughput sequencing of the amoA gene coding the ammonia monooxygenase enzyme active subunit, and sediment slurry incubation experiments. AOB abundance ranged from 8.54 × 10 4 to 5.85 × 10 6 copies g -1 of wet sediment weight and exhibited an increasing trend from the Liaohe Estuary to the open coastal zone. Potential nitrification rates (PNRs) ranged from 0.1 to 336.8 nmol N g -1 day -1 along the estuary to the coastal zone. Log AOB abundance and PNRs were significantly positively correlated. AOB richness decreased from the estuary to the coastal zone. High-throughput sequencing analysis indicated that the majority of amoA gene sequences fell within the Nitrosomonas and Nitrosomonas-like clade, and only a few sequences were clustered within the Nitrosospira clade. This finding indicates that the Nitrosomonas-related lineage may be more adaptable to the specific conditions in this estuary than the Nitrosospira lineage. Sites with high nitrification rates were located in the southern open region and were dominated by the Nitrosomonas-like lineage, whereas the Nitrosospira lineage was found primarily in the northern estuary mouth sites with low nitrification rates. Thus, nitrification potentials in Liaohe estuarine sediments in the southern open region were greater than those in the northern estuary mouth, and the Nitrosomonas-related lineage might play a more important role than the Nitrosospira lineage in nitrification in this estuary.

  3. Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea.

    PubMed

    Pizzetti, Ilaria; Fuchs, Bernhard M; Gerdts, Gunnar; Wichels, Antje; Wiltshire, Karen H; Amann, Rudolf

    2011-07-01

    Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ~90% of the Planctomycetes reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.

  4. Spatial patterns in the abundance of the coastal horned lizard

    USGS Publications Warehouse

    Fisher, Robert N.; Suarez, Andrew V.; Case, Ted J.

    2002-01-01

    Coastal horned lizards (   Phrynosoma coronatum) have undergone severe declines in southern California and are a candidate species for state and federal listing under the Endangered Species Act. Quantitative data on their habitat use, abundance, and distribution are lacking, however. We investigated the determinants of abundance for coastal horned lizards at multiple spatial scales throughout southern California. Specifically, we estimated lizard distribution and abundance by establishing 256 pitfall trap arrays clustered within 21 sites across four counties. These arrays were sampled bimonthly for 2–3 years. At each array we measured 26 “local” site descriptors and averaged these values with other “regional” measures to determine site characteristics. Our analyses were successful at identifying factors within and among sites correlated with the presence and abundance of coastal horned lizards. These factors included the absence of the invasive Argentine ant (  Linepithema humile) (and presence of native ant species eaten by the lizards), the presence of chaparral community plants, and the presence of sandy substrates. At a regional scale the relative abundance of Argentine ants was correlated with the relative amount of developed edge around a site. There was no evidence for spatial autocorrelation, even at the scale of the arrays within sites, suggesting that the determinants of the presence or absence and abundance of horned lizard can vary over relatively small spatial scales ( hundreds of meters). Our results suggest that a gap-type approach may miss some of the fine-scale determinants of species abundance in fragmented habitats.

  5. Variable depth distribution of Trichodesmium clades in the North Pacific Ocean.

    PubMed

    Rouco, Mónica; Haley, Sheean T; Alexander, Harriet; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

    2016-12-01

    Populations of nitrogen-fixing cyanobacteria in the genus Trichodesmium are critical to ocean ecosystems, yet predicting patterns of Trichodesmium distribution and their role in ocean biogeochemistry is an ongoing challenge. This may, in part, be due to differences in the physiological ecology of Trichodesmium species, which are not typically considered independently in field studies. In this study, the abundance of the two dominant Trichodesmium clades (Clade I and Clade III) was investigated during a survey at Station ALOHA in the North Pacific Subtropical Gyre (NPSG) using a clade-specific qPCR approach. While Clade I dominated the Trichodesmium community, Clade III abundance was >50% in some NPSG samples, in contrast to the western North Atlantic where Clade III abundance was always <10%. Clade I populations were distributed down to depths >80 m, while Clade III populations were only observed in the mixed layer and found to be significantly correlated with depth and temperature. These data suggest active niche partitioning of Trichodesmium species from different clades, as has been observed in other cyanobacteria. Tracking the distribution and physiology of Trichodesmium spp. would contribute to better predictions of the physiological ecology of this biogeochemically important genus in the present and future ocean. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

    PubMed

    Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

    2016-10-01

    For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

  7. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sowell, Sarah; Abraham, Paul E; Shah, Manesh B

    2011-01-01

    Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the o 1.2 lm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% ofmore » all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.« less

  8. Relative abundance and size of coastal sharks derived from commercial shark longline catch and effort data.

    PubMed

    Carlson, J K; Hale, L F; Morgan, A; Burgess, G

    2012-04-01

    In the north-west Atlantic Ocean, stock assessments conducted for some commercially harvested coastal sharks indicate declines from 64 to 80% with respect to virgin population levels. While the status of commercially important species is available, abundance trend information for other coastal shark species in the north-west Atlantic Ocean are unavailable. Using a generalized linear modelling (GLM) approach, a relative abundance index was derived from 1994 to 2009 using observer data collected in a commercial bottom longline fishery. Trends in abundance and average size were estimated for bull shark Carcharhinus leucas, spinner shark Carcharhinus brevipinna, tiger shark Galeocerdo cuvier and lemon shark Negaprion brevirostris. Increases in relative abundance for all shark species ranged from 14% for C. brevipinna, 12% for C. leucas, 6% for N. brevirostris and 3% for G. cuvier. There was no significant change in the size at capture over the time period considered for all species. While the status of shark populations should not be based exclusively on abundance trend information, but ultimately on stock assessment models, results from this study provide some cause for optimism on the status of these coastal shark species. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

  9. Seasonal Diversity Patterns of a Coastal Synechococcus Population

    NASA Astrophysics Data System (ADS)

    Hunter-Cevera, K. R.; Sosik, H. M.; Neubert, M.; Hammar, K.; Post, A.

    2016-02-01

    Understanding how environmental and ecological factors determine phytoplankton species abundances requires knowledge of the diversity present within a population. For the important primary producer Synechococcus, clades demonstrate differences in temperature tolerance, light acclimation, grazer palatability, and more. Marine Synechococcus populations are often composed of more than one clade, and overall population dynamics will be governed by the types of cells present and by their individual physiological capabilities. We investigate the diversity of the Synechococcus assemblage at the Martha's Vineyard Coastal Observatory with high-throughput sequencing of the V6 hypervariable region of the 16S rRNA gene. Small nucleotide differences within this region allow for resolution of distinct phylotypes that can have a direct correspondence to the well-defined Synechococcus clades. From a three-year time series, we find that the Synechococcus population is dominated by 5 distinct phylotypes, and that each type exhibits a repeatable, seasonal pattern in relative abundance. We use compositional data analysis techniques to investigate the relationships between these patterns and environmental factors. We further interpret these patterns in the context of Synechococcus population dynamics assessed by automated, submersible flow cytometry (FlowCytobot). Observed diel changes in cell size distributions, coupled with a validated matrix population model, provide estimates of in situ population division rates. We find strong evidence that the main seasonal diversity patterns are governed by temperature, but that biological loss agents likely shape the diversity structure for certain times of year. For some phylotypes, relative abundance patterns are also related to light and nutrients. The composition of Synechococcus over the annual cycle appears to directly affect seasonal features of cell abundance patterns, such as the spring bloom.

  10. Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

    PubMed Central

    Rappé, Michael S.

    2013-01-01

    In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

  11. Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

    PubMed Central

    He, Yaodong; Sen, Biswarup; Zhou, Shuangyan; Xie, Ningdong; Zhang, Yongfeng; Zhang, Jianle; Wang, Guangyi

    2017-01-01

    Qinhuangdao coastal waters in northern China are heavily impacted by anthropogenic and natural activities, and we anticipate a direct influence of the impact on the bacterioplankton abundance and diversity inhabiting the adjacent coastal areas. To ascertain the anthropogenic influences, we first evaluated the seasonal abundance patterns and diversity of bacterioplankton in the coastal areas with varied levels of natural and anthropogenic activities and then analyzed the environmental factors which influenced the abundance patterns. Results indicated distinct patterns in bacterioplankton abundance across the warm and cold seasons in all stations. Total bacterial abundance in the stations ranged from 8.67 × 104 to 2.08 × 106 cells/mL and had significant (p < 0.01) positive correlation with total phosphorus (TP), which indicated TP as the key monitoring parameter for anthropogenic impact on nutrients cycling. Proteobacteria and Cyanobacteria were the most abundant phyla in the Qinhuangdao coastal waters. Redundancy analysis revealed significant (p < 0.01) influence of temperature, dissolved oxygen and chlorophyll a on the spatiotemporal abundance pattern of α-Proteobacteria and Cyanobacteria groups. Among the 19 identified bacterioplankton subgroups, α-Proteobacteria (phylum Proteobacteria) was the dominant one followed by Family II (phylum Cyanobacteria), representing 19.1–55.2% and 2.3–54.2% of total sequences, respectively. An inverse relationship (r = -0.82) was observed between the two dominant subgroups, α-Proteobacteria and Family II. A wide range of inverse Simpson index (10.2 to 105) revealed spatial heterogeneity of bacterioplankton diversity likely resulting from the varied anthropogenic and natural influences. Overall, our results suggested that seasonal variations impose substantial influence on shaping bacterioplankton abundance patterns. In addition, the predominance of only a few cosmopolitan species in the Qinhuangdao coastal wasters was

  12. The effects of coastal development on sponge abundance, diversity, and community composition on Jamaican coral reefs.

    PubMed

    Stubler, Amber D; Duckworth, Alan R; Peterson, Bradley J

    2015-07-15

    Over the past decade, development along the northern coast of Jamaica has accelerated, resulting in elevated levels of sedimentation on adjacent reefs. To understand the effects of this development on sponge community dynamics, we conducted surveys at three locations with varying degrees of adjacent coastal development to quantify species richness, abundance and diversity at two depths (8-10 m and 15-18 m). Sediment accumulation rate, total suspended solids and other water quality parameters were also quantified. The sponge community at the location with the least coastal development and anthropogenic influence was often significantly different from the other two locations, and exhibited higher sponge abundance, richness, and diversity. Sponge community composition and size distribution were statistically different among locations. This study provides correlative evidence that coastal development affects aspects of sponge community ecology, although the precise mechanisms are still unclear. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Can functional equivalency between seagrasses and other coastal habitats offset loss of ecosystem health with reduced seagrass abundance?

    NASA Astrophysics Data System (ADS)

    Cebrian, J.; Anton, A.; Christiaen, B.; Gamble, R.; Stutes, J.

    2016-02-01

    Seagrasses provide important ecosystem services, such as habitat for fisheries, shoreline stabilization, pollution filtration, and carbon sequestration. Thus, seagrass loss may seriously compromise coastal ecosystem services worldwide. However, functional equivalency (or redundancy) between seagrasses and other components of coastal ecosystems, such as algae and marshes, can offset the loss of services under declining seagrass abundance. That is, if seagrasses are redundant with algae and marshes in their functionality, then ecosystem services may be preserved in changing coasts with declining seagrass but pervading algal and marsh communities. Here we present several instances of functional redundancy between seagrasses and other coastal components in the Northern Gulf of Mexico. We first examine how net ecosystem production, which sets a limit to carbon accumulation and export to neighbouring communities, changes with eutrophication-induced seagrass decline and concomitant increase in algal abundance. Results from comparative and manipulative field studies are congruent and show no change in net ecosystem production despite drastic shifts from seagrass to algal dominance. We further provide evidence that fringing marshes can counteract the reduction in habitat provision for structure-dependent fisheries due to seagrass loss. Using a large-scale field comparison we show that, as long as fringing marshes are preserved, the abundance and diversity of structure-dependent fisheries are maintained despite large seagrass loss. Functional redundancy for habitat provision also occurs between seagrasses and well-oxygenated macroagal stands, since canopy-dwelling faunal abundance remains unaltered if seagrasses are replaced by normoxic algal stands. In concert the results demonstrate substantial functional equivalency between seagrasses and other coastal components, and indicate seagrass loss does not necessarily result in depressed coastal ecosystem health and services.

  14. FISH-Flow: a quantitative molecular approach for describing mixed clade communities of Symbiodinium

    NASA Astrophysics Data System (ADS)

    McIlroy, S. E.; Smith, G. J.; Geller, J. B.

    2014-03-01

    Our understanding of reef corals and their fate in a changing climate is limited by our ability to monitor the diversity and abundance of the dinoflagellate endosymbionts that sustain them. This study combined two well-known methods in tandem: fluorescent in situ hybridization (FISH) for genotype-specific labeling of Symbiodinium and flow cytometry to quantify the abundance of each symbiont clade in a sample. This technique (FISH-Flow) was developed with cultured Symbiodinium representing four distinct clades (based on large subunit rDNA) and was used to distinguish and quantify these types with high efficiency and few false positives. This technique was also applied to freshly isolated symbionts of Orbicella faveolata and Orbicella annularis. Isolates from acutely bleached coral tissues had significantly lower labeling efficiency; however, isolates from healthy tissue had efficiencies comparable to cultured Symbiodinium trials. RNA degradation in bleaching samples may have interfered with labeling of cells. Nevertheless, we were able to determine that, with and without thermal stress, experimental columns of the coral O. annularis hosted a majority of clade B and B/C symbionts on the top and side of the coral column, respectively. We demonstrated that, for cultured Symbiodinium and Symbiodinium freshly isolated from healthy host tissues, the relative ratio of clades could be accurately determined for clades present at as low as 7 % relative abundance. While this method does not improve upon PCR-based techniques in identifying clades at background levels, FISH-Flow provides a high precision, flexible system for targeting, quantifying and isolating Symbiodinium genotypes of interest.

  15. Grazer Impacts on Synechococcus Populations in the Coastal Gulf of Maine; Identifying Specific Microbial Interactions to Understand Bloom Dynamics

    NASA Astrophysics Data System (ADS)

    Countway, P. D.; Poulton, N.; Sieracki, M.; Hoeglund, A.; Anderson, S.; Burns, W. G.

    2016-02-01

    Protistan grazers help to shape the diversity, abundance, and composition of bacterial and phytoplankton communities, yet very little is known about the specific interactions between grazers and their prey. Grazers play key roles in the demise of phytoplankton blooms, with the abundance of grazers often increasing dramatically as prey-species decline. The timing and fate of Synechococcus blooms was investigated over a two-year period in Booth Bay, Maine (USA). The Synechococcus bloom in this region is characterized by several peaks in cell abundance, followed by periods of rapid decline. Two clades of Synechococcus (rpoC1 gene clades I and IV) were detected at our study site, with clade I typically present at higher abundance than clade IV. Modified grazing experiments were conducted at different stages of the Synechococcus bloom in which the natural plankton community was diluted with either 0.45 µm (grazer-free) or 30 kDa (grazer- and virus-free) filtered seawater. In general, the impact of grazers on Synechococcus populations was greater than the impact due to encounters with viruses during 24-hour in situ incubations. Interactions between grazers and Synechococcus were investigated using Fluorescence Activated Cell Sorting (FACS) combined with single-cell genomics to identify specific associations between sorted-grazers and their prey. Single-cell sequencing revealed a diverse array of heterotrophic protists on sampling dates that occurred after periods of rapid decrease in the abundance of Synechococcus. Cultures of Synechococcus were added to natural plankton communities to stimulate grazers, which were subsequently cell-sorted in bulk mode and sequenced. These experiments revealed similar taxonomic affiliations of putative grazer types (e.g., Cercozoa) that responded to the presence of Synechococcus prey. Protistan grazers appear to exert a strong degree of control on the abundance and duration of the annual Synechococcus bloom in the coastal Gulf of Maine.

  16. Exceptionally high abundances of microplastics in the oligotrophic Israeli Mediterranean coastal waters.

    PubMed

    van der Hal, Noam; Ariel, Asaf; Angel, Dror L

    2017-03-15

    Seasonal sea surface microplastic distribution was recorded at 17 sites along the Israeli Mediterranean coast. Microplastics (0.3-5mm) were found in all samples, with a mean abundance of 7.68±2.38particles/m 3 or 1,518,340particles/km 2 . Some areas had higher abundances of microplastics than others, although differences were neither consistent nor statistically significant. In some cases microplastic particles were found floating in large patches. One of these patches contained an extraordinary number of plastic particles; 324particles/m 3 or 64,812,600particles/km 2 . Microplastic abundances in Israeli coastal waters are disturbingly high; mean values were 1-2 orders of magnitude higher than abundances reported in other parts of the world. Light-colored (white or transparent) fragments were by far more abundant than all other microplastic colors and types. The results of this study underline the need for action to reduce the flux of plastics to the marine environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

    PubMed

    Wear, Emma K; Wilbanks, Elizabeth G; Nelson, Craig E; Carlson, Craig A

    2018-03-09

    Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3.

    PubMed

    Bhattarai, Susma; Cassarini, Chiara; Gonzalez-Gil, Graciela; Egger, Matthias; Slomp, Caroline P; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

    2017-10-01

    The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

  19. Rates of Dinitrogen Fixation and the Abundance of Diazotrophs in North American Coastal Waters Between Cape Hatteras and Georges Bank

    NASA Technical Reports Server (NTRS)

    Mulholland, M.R.; Bernhardt, P. W.; Blanco-Garcia, J. L.; Mannino, A.; Hyde, K.; Mondragon, E.; Turk, K.; Moisander, P. H.; Zehr, J. P.

    2012-01-01

    We coupled dinitrogen (N2) fixation rate estimates with molecular biological methods to determine the activity and abundance of diazotrophs in coastal waters along the temperate North American Mid-Atlantic continental shelf during multiple seasons and cruises. Volumetric rates of N2 fixation were as high as 49.8 nmol N L(sup -1) d(sup -1) and areal rates as high as 837.9 micromol N m(sup -2) d(sup -1) in our study area. Our results suggest that N2 fixation occurs at high rates in coastal shelf waters that were previously thought to be unimportant sites of N2 fixation and so were excluded from calculations of pelagic marine N2 fixation. Unicellular N2-fixing group A cyanobacteria were the most abundant diazotrophs in the Atlantic coastal waters and their abundance was comparable to, or higher than, that measured in oceanic regimes where they were discovered. High rates of N2 fixation and the high abundance of diazotrophs along the North American Mid-Atlantic continental shelf highlight the need to revise marine N budgets to include coastal N2 fixation. Integrating areal rates of N2 fixation over the continental shelf area between Cape Hatteras and Nova Scotia, the estimated N2 fixation in this temperate shelf system is about 0.02 Tmol N yr(sup -1), the amount previously calculated for the entire North Atlantic continental shelf. Additional studies should provide spatially, temporally, and seasonally resolved rate estimates from coastal systems to better constrain N inputs via N2 fixation from the neritic zone.

  20. A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades.

    PubMed

    Brown, Mark V; Ostrowski, Martin; Grzymski, Joseph J; Lauro, Federico M

    2014-06-01

    Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa. Copyright © 2014. Published by Elsevier B.V.

  1. Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

    PubMed Central

    Taylor, Joe D; Cunliffe, Michael

    2016-01-01

    Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623

  2. Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII.

    PubMed

    Lopes Dos Santos, Adriana; Gourvil, Priscillia; Rodríguez, Francisco; Garrido, José Luis; Vaulot, Daniel

    2016-02-01

    The ecological importance and diversity of pico/nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis. © 2015 Phycological Society of America.

  3. Abundance and Distribution Characteristics of Microplastics in Surface Seawaters of the Incheon/Kyeonggi Coastal Region.

    PubMed

    Chae, Doo-Hyeon; Kim, In-Sung; Kim, Seung-Kyu; Song, Young Kyoung; Shim, Won Joon

    2015-10-01

    Microplastics in marine environments are of emerging concern due to their widespread distribution, their ingestion by various marine organisms, and their roles as a source and transfer vector of toxic chemicals. However, our understanding of their abundance and distribution characteristics in surface seawater (SSW) remains limited. We investigated microplastics in the surface microlayer (SML) and the SSW at 12 stations near-shore and offshore of the Korean west coast, Incheon/Kyeonggi region. Variation between stations, sampling media, and sampling methods were compared based on abundances, size distribution, and composition profiles of microsized synthetic polymer particles. The abundance of microplastics was greater in the SML (152,688 ± 92,384 particles/m(3)) than in SSW and showed a significant difference based on the sampling method for SSWs collected using a hand net (1602 ± 1274 particles/m(3)) and a zooplankton trawl net (0.19 ± 0.14 particles/m(3)). Ship paint particles (mostly alkyd resin polymer) accounted for the majority of microplastics detected in both SML and SSWs, and increased levels were observed around the voyage routes of large vessels. This indicates that polymers with marine-based origins become an important contributor to microplastics in coastal SSWs of this coastal region.

  4. Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons.

    PubMed

    Junger, Pedro C; Amado, André M; Paranhos, Rodolfo; Cabral, Anderson S; Jacques, Saulo M S; Farjalla, Vinicius F

    2018-01-01

    Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m -1 ), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 μg L -1 ). Virus abundance varied from 0.37 × 10 8 to 117 × 10 8 virus-like-particle (VLP) mL -1 , with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 10 7 to 56.5 × 10 7 VLP mL -1 h -1 and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.

  5. The Abundance of Pink-Pigmented Facultative Methylotrophs in the Root Zone of Plant Species in Invaded Coastal Sage Scrub Habitat

    PubMed Central

    Irvine, Irina C.; Brigham, Christy A.; Suding, Katharine N.; Martiny, Jennifer B. H.

    2012-01-01

    Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C1 compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 102 to 105 CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems. PMID:22383990

  6. The abundance of pink-pigmented facultative methylotrophs in the root zone of plant species in invaded coastal sage scrub habitat.

    PubMed

    Irvine, Irina C; Brigham, Christy A; Suding, Katharine N; Martiny, Jennifer B H

    2012-01-01

    Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C(1) compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 10(2) to 10(5) CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems.

  7. Estimating growth rates of uncultivated clades of archaea and bacteria in marine sediments

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.

    2016-12-01

    The vast majority of microbes present in marine sediments have never been cultivated in laboratory conditions. It is therefore difficult to estimate the growth rates of these organisms in situ. Quantitative PCR (qPCR) and 16S rRNA gene libraries from sediments below 10 cm show very little change in abundance of these organisms with depth or with redox conditions. Therefore, we hypothesized that uncultivated clades of bacteria and archaea that are ubiquitous in marine sediments, actually grow in the upper 10 cm of marine sediments. We collected sediment cores from the White Oak River estuary, sectioned them in 1 cm intervals, and examined the changes in abundance of uncultivated microbes with depth using 16S rRNA gene libraries and qPCR. We found that some of the key clades associated with the deep subsurface microbiome, such as Bathyarchaeota and MBG-D, increase in abundance with depth, demonstrating extremely slow growth in these shallow subsurface sediments.

  8. Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

    PubMed Central

    Marietou, Angeliki

    2014-01-01

    Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. PMID:25063663

  9. Comparison of the seasonal variability in abundance of the copepod Pseudocalanus newmani in Lagoon Notoro-ko and a coastal area of the southwestern Okhotsk Sea

    NASA Astrophysics Data System (ADS)

    Kitamura, Mitsuaki; Nakagawa, Yoshizumi; Nishino, Yasuto; Segawa, Susumu; Shiomoto, Akihiro

    2018-03-01

    Replacement of the warm water of the Soya Warm Current (SWC) and the cold water of the East Sakhalin Current (ESC) occurs seasonally along the coast of the southwestern Okhotsk Sea, and sea ice covers the surface during winter. Pseudocalanus newmani is one of the dominant copepods in coastal waters of the northern hemisphere. To better understand the population dynamics of the copepod P. newmani in coastal areas of the southwestern Okhotsk Sea, this study compared the seasonal variation in P. newmani abundance in Lagoon Notoro-ko and a coastal area of the Okhotsk Sea with regard to developmental stage. We sampled P. newmani in the lagoon, including during the ice cover season, and the coastal waters. Pseudocalanus newmani was abundant at both sites in spring. During summer-fall, adults disappeared from the populations at both sites, whereas the early developmental stages were abundant and dominated the population. Total length of adult females decreased toward summer at both sites. Pseudocalanus newmani abundance in the lagoon increased in early winter, and larger females were found in the populations at both sites. These phenomena at both sites corresponded with seasonal variation in water temperature caused by seasonal water-mass replacement and sea ice.

  10. Genetic recombination events between sympatric Clade A and Clade C lice in Africa.

    PubMed

    Veracx, Aurélie; Boutellis, Amina; Raoult, Didier

    2013-09-01

    Human head and body lice have been classified into three phylogenetic clades (Clades A, B, and C) based on mitochondrial DNA. Based on nuclear markers (the 18S rRNA gene and the PM2 spacer), two genotypes of Clade A head and body lice, including one that is specifically African (Clade A2), have been described. In this study, we sequenced the PM2 spacer of Clade C head lice from Ethiopia and compared these sequences with sequences from previous works. Trees were drawn, and an analysis of genetic diversity based on the cytochrome b gene and the PM2 spacer was performed for African and non-African lice. In the tree drawn based on the PM2 spacer, the African and non-African lice formed separate clusters. However, Clade C lice from Ethiopia were placed within the African Clade A subcluster (Clade A2). This result suggests that recombination events have occurred between Clade A2 lice and Clade C lice, reflecting the sympatric nature of African lice. Finally, the PM2 spacer and cytochrome b gene sequences of human lice revealed a higher level of genetic diversity in Africa than in other regions.

  11. Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

    PubMed Central

    Simmons, Melinda P.; Sudek, Sebastian; Monier, Adam; Limardo, Alexander J.; Jimenez, Valeria; Perle, Christopher R.; Elrod, Virginia A.; Pennington, J. Timothy

    2016-01-01

    Eukaryotic algae within the picoplankton size class (≤2 μm in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus, during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 × 105 and 3.37 × 105 cells · ml−1, respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 × 105 cells · ml−1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 ± 327 18S rRNA gene copies · ml−1. Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos) and BII. These share 82% ± 6% nucleotide identity across homologs, while the Ostreococcus spp. share 75% ± 8%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO3− and low-affinity NH4+ transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in

  12. Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean.

    PubMed

    Simmons, Melinda P; Sudek, Sebastian; Monier, Adam; Limardo, Alexander J; Jimenez, Valeria; Perle, Christopher R; Elrod, Virginia A; Pennington, J Timothy; Worden, Alexandra Z

    2016-01-04

    Eukaryotic algae within the picoplankton size class (≤2 μm in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus, during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 × 10(5) and 3.37 × 10(5) cells · ml(-1), respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 × 10(5) cells · ml(-1) in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 ± 327 18S rRNA gene copies · ml(-1). Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos) and BII. These share 82% ± 6% nucleotide identity across homologs, while the Ostreococcus spp. share 75% ± 8%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO3 (-) and low-affinity NH4 (+) transporters, respectively, with close homologs in multiple picoprasinophytes

  13. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

    PubMed

    Dyksma, Stefan; Bischof, Kerstin; Fuchs, Bernhard M; Hoffmann, Katy; Meier, Dimitri; Meyerdierks, Anke; Pjevac, Petra; Probandt, David; Richter, Michael; Stepanauskas, Ramunas; Mußmann, Marc

    2016-08-01

    Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.

  14. Expanding the World of Marine Bacterial and Archaeal Clades

    PubMed Central

    Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

    2016-01-01

    Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as

  15. Genetic tools for the investigation of Roseobacter clade bacteria

    PubMed Central

    2009-01-01

    Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria. PMID:20021642

  16. Marine debris in beaches of the Southwestern Atlantic: An assessment of their abundance and mass at different spatial scales in northern coastal Argentina.

    PubMed

    Becherucci, Maria Eugenia; Rosenthal, Alan Federico; Seco Pon, Juan Pablo

    2017-06-15

    Argentina is currently undergoing an intensive development of coastal-oriented tourism due to the temperate climate and coastal sceneries of the Southwestern Atlantic and particularly its wide ocean-open sandy beaches, which may turn into an important contributor of marine debris to the beaches. This study was designed to assess at four spatial scales (i) the variation of the abundance and mass of marine debris and (ii) the composition and sources of these items in sandy-tourist beaches of coastal zones of the province of Buenos Aires, in northern Argentina. The abundance and mass of marine debris shifted between sampling localities (separated by ~1.5×10 5 m) and beaches (~3×10 4 m). Debris was primarily from recreational and fishing activities and over 20mm in size. Tackling the complications associated with marine debris in northern Argentina may include intensive educational and advertising campaigns oriented chiefly to beach users and fisherman. Copyright © 2017. Published by Elsevier Ltd.

  17. Temporal Variation in Black Sea Bass (Centropristis striata) Abundance in the Maryland Coastal Bays

    NASA Astrophysics Data System (ADS)

    Peters, R.; Chigbu, P.

    2016-02-01

    Black sea bass (Centropristis striata) is a warm temperate species associated with structured habitats along the Atlantic Coast of the United States. Currently, the northern stock is considered data poor, and the lack of information about the abundance and ecology of these fish in estuaries is a major concern. The Maryland Coastal Bays (MCBs) serves as a habitat for 0+ and 1+ black sea bass. The Maryland Department of Natural Resources conducts annual surveys of juvenile finfish including black sea bass in the MCBs from April to October. Highest mean Catch-Per-Unit efforts (CPUE) were in sites 7 (Isle of Wight Bay), 9 (Sinepuxent Bay), and 20 (Chincoteague Bay), which are also sites closet to the Ocean City and Chincoteague Inlets. Length frequency distribution from data collected from 1989-2013 in these trawls show that there are two year classes in the MCBs. Juveniles (1+) began to enter the bays in April, and (YoY) 0+ fish were caught in the trawls beginning in June. Juvenile abundance peaked in July, while 0+ abundance peaked in September. The abundance of both 0+ and 1+ fish varied over the years with abundances peaking in the same years. YoY black sea bass abundance was positively correlated (r2=0.22, p≤0.05) with average salinity each year and negatively correlated (r2=0.15, p≤0.05) with average NAO winter index. The negative NAO winter years could cause the increase in salinity, which could favor high recruitment. This could be caused by the warmer winters increasing rainfall and reducing salinity during that time. However, abundance of YoY was low in the MCBs, which could be from the trawl gear used to sample the structure oriented fish, and therefore could be a source of bias in this study. Nevertheless, other studies have also used trawls to assess distribution and trends of YoY black sea bass. Studies using traps to assess the relative abundance of the fish in the MCBs are ongoing, and could provide more insight into climatic factors affecting

  18. Evidence that clade A and clade B head lice live in sympatry and recombine in Algeria.

    PubMed

    Boutellis, A; Bitam, I; Fekir, K; Mana, N; Raoult, D

    2015-03-01

    Pediculus humanus L. (Psocodea: Pediculidae) can be characterized into three deeply divergent lineages (clades) based on mitochondrial DNA. Clade A consists of both head lice and clothing lice and is distributed worldwide. Clade B consists of head lice only and is mainly found in North and Central America, and in western Europe and Australia. Clade C, which consists only of head lice, is found in Ethiopia, Nepal and Senegal. Twenty-six head lice collected from pupils at different elementary schools in two localities in Algiers (Algeria) were analysed using molecular methods for genotyping lice (cytochrome b and the multi-spacer typing (MST) method. For the first time, we found clade B head lice in Africa living in sympatry with clade A head lice. The phylogenetic analysis of the concatenated sequences of these populations of head lice showed that clade A and clade B head lice had recombined, suggesting that interbreeding occurs when lice live in sympatry. © 2014 The Royal Entomological Society.

  19. The relative importance of disturbance and exotic-plant abundance in California coastal sage scrub

    USGS Publications Warehouse

    Fleming, G.M.; Diffendorfer, J.E.; Zedler, P.H.

    2009-01-01

    Many ecosystems of conservation concern require some level of disturbance to sustain their species composition and ecological function. However, inappropriate disturbance regimes could favor invasion or expansion of exotic species. In southern California coastal sage scrub (CSS) fire is a natural disturbance, but because of human influence, frequencies may now be unnaturally high. Other anthropogenic disturbances such as grazing also occur in reserve areas. Managers charged with imposing or tolerating fire or other disturbance within their reserves are concerned that habitat quality may be degraded by an increasing abundance of exotic plants. We used vegetation monitoring data from Camp Pendleton, California, USA, to assess the correlation between past disturbances (frequent fire, agriculture, or grazing and mechanical disturbances) and current exotic species abundance in CSS. We found that disturbance history was only modestly related to exotic abundance overall, but fire frequency showed the strongest association. We also examined whether cover and richness of various native plant life forms (woody species, perennial herbs, and annual herbs) were more strongly influenced by disturbance history or by exotic-plant abundance. Native plant responses varied among life forms, but woody species and annual herbs were generally more strongly and negatively associated with exotic abundance than with disturbance. Effective CSS conservation will require developing means to curb the negative impacts of exotic plants, which may abound with or without severe or recent disturbance. Additionally, more focus should be given to understory herbs showing sensitivity to invasion. Though understudied, native herbs comprise the greatest portion of plant diversity in CSS and are critical to preservation of the community as a whole. ?? 2009 by the Ecological Society of America.

  20. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems.

    PubMed

    Rappé; Vergin; Giovannoni

    2000-09-01

    In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of beta Proteobacteria related to those found in clone libraries from freshwater habitats. beta Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. In addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the alpha subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats.

  1. Capture-recapture abundance and survival estimates of three cetacean species in Icelandic coastal waters using trained scientist-volunteers

    NASA Astrophysics Data System (ADS)

    Bertulli, Chiara G.; Guéry, Loreleï; McGinty, Niall; Suzuki, Ailie; Brannan, Naomi; Marques, Tania; Rasmussen, Marianne H.; Gimenez, Olivier

    2018-01-01

    Knowledge of abundance and survival of humpback whales, white-beaked dolphins and minke whales are essential to manage and conserve these species in Icelandic coastal shelf waters. Our main goal was to test the feasibility of employing inexpensive research methods (data collected by trained-scientist volunteers onboard opportunistic vessels) to assess abundance and apparent survival. No previous studies in Iceland have investigated these two demographic parameters in these three cetacean species using open capture-recapture models accounting for imperfect and possibly heterogeneous detection. A transient effect was accounted for whenever required to estimate the population of resident individuals. Identification photographs were collected by scientist-trained volunteers for 7 years (2006-2013) from onboard commercial whale-watching vessels in the coastal waters of Faxaflói (southwest coast, 4400 km2) and Skjálfandi (northeast coast, 1100 km2), Iceland. We estimated an average abundance of 83 humpback whales (Mn; 95% confidence interval: 54-130) in Skjálfandi; 238 white-beaked dolphins (La; [163-321]) in Faxaflói; and 67 minke whales (Ba; [53-82]) in Faxaflói and 24 (14-31) in Skjálfandi. We also found that apparent survival was constant for all three species (Mn: 0.52 [0.41-0.63], La: 0.79 [0.64-0.88], Ba-Faxaflói: 0.80 [0.67-0.88], Ba-Skjálfandi: 0.96 [0.60-0.99]). Our results showed inter-annual variation in abundance estimates which were small for all species, and the presence of transience for minke whales. A significant increase in abundance during the study period was solely found in minke whale data from Skjálfandi. Humpback whales and white-beaked dolphins showed lower apparent survival rates compared to similar baleen whale and dolphin populations. Our results show data collected by trained-scientist volunteers can produce viable estimates of abundance and survival although bias in the methods we employed exist and need to be addressed. With the

  2. Highly pathogenic avian influenza H5N1 clade 2.3.2.1 and clade 2.3.4 viruses do not induce a clade-specific phenotype in mallard ducks

    PubMed Central

    Crumpton, Jeri Carol; Rubrum, Adam; Phommachanh, Phouvong; Douangngeun, Bounlom; Peiris, Malik; Guan, Yi; Webster, Robert; Webby, Richard

    2017-01-01

    Among the diverse clades of highly pathogenic avian influenza (HPAI) H5N1 viruses of the goose/Guangdong lineage, only a few have been able to spread across continents: clade 2.2 viruses spread from China to Europe and into Africa in 2005–2006, clade 2.3.2.1 viruses spread from China to Eastern Europe in 2009–2010 and clade 2.3.4.4 viruses of the H5Nx subtype spread from China to Europe and North America in 2014/2015. While the poultry trade and wild-bird migration have been implicated in the spread of HPAI H5N1 viruses, it has been proposed that robust virus-shedding by wild ducks in the absence of overt clinical signs may have contributed to the wider dissemination of the clade 2.2, 2.3.2.1 and 2.3.4.4 viruses. Here we determined the phenotype of two divergent viruses from clade 2.3.2.1, a clade that spread widely, and two divergent viruses from clade 2.3.4, a clade that was constrained to Southeast Asia, in young (ducklings) and adult (juvenile) mallard ducks. We found that the virus-shedding magnitude and duration, transmission pattern and pathogenicity of the viruses in young and adult mallard ducks were largely independent of the virus clade. A clade-specific pattern could only be detected in terms of cumulative virus shedding, which was higher with clade 2.3.2.1 than with clade 2.3.4 viruses in juvenile mallards, but not in ducklings. The ability of clade 2.3.2.1c A/common buzzard/Bulgaria/38 WB/2010-like viruses to spread cross-continentally may, therefore, have been strain-specific or independent of phenotype in wild ducks. PMID:28631606

  3. Abundance and Size of Gulf Shrimp in Louisiana's Coastal Estuaries following the Deepwater Horizon Oil Spill

    PubMed Central

    van der Ham, Joris L.; de Mutsert, Kim

    2014-01-01

    The Deepwater Horizon oil spill impacted Louisiana's coastal estuaries physically, chemically, and biologically. To better understand the ecological consequences of this oil spill on Louisiana estuaries, we compared the abundance and size of two Gulf shrimp species (Farfantepeneus aztecus and Litopeneus setiferus) in heavily affected and relatively unaffected estuaries, before and after the oil spill. Two datasets were used to conduct this study: data on shrimp abundance and size before the spill were available from Louisiana Department of Wildlife and Fisheries (LDWF). Data on shrimp abundance and size from after the spill were independently collected by the authors and by LDWF. Using a Before-After-Control-Impact with Paired sampling (BACIP) design with monthly samples of two selected basins, we found brown shrimp to become more abundant and the mean size of white shrimp to become smaller. Using a BACIP with data on successive shrimp year-classes of multiple basins, we found both species to become more abundant in basins that were affected by the spill, while mean shrimp size either not change after the spill, or increased in both affected and unaffected basins. We conclude that following the oil spill abundances of both species increased within affected estuaries, whereas mean size may have been unaffected. We propose two factors that may have caused these results: 1) exposure to polycyclic aromatic hydrocarbons (PAHs) may have reduced the growth rate of shrimp, resulting in a delayed movement of shrimp to offshore habitats, and an increase of within-estuary shrimp abundance, and 2) fishing closures established immediately after the spill, may have resulted in decreased fishing effort and an increase in shrimp abundance. This study accentuates the complexities in determining ecological effects of oil spills, and the need of studies on the organismal level to reveal cause-and-effect relationships of such events. PMID:25272142

  4. Partitioning Nitrification Between Specific Archaeal and Bacterial Clades in a Large, Nitrogen-Rich Estuary (San Francisco Bay, CA)

    NASA Astrophysics Data System (ADS)

    Damashek, J.; Casciotti, K. L.; Francis, C. A.

    2014-12-01

    Nitrification is the sole link between nitrogen inputs and losses in marine ecosystems, and understanding the microbial ecology and biogeochemistry of nitrification is therefore crucial for understanding how aquatic ecosystems process nitrogen. Recently-discovered ammonia-oxidizing archaea (AOA), rather than ammonia-oxidizing bacteria (AOB), appear to drive ammonia oxidation in many ecosystems, including much of the ocean. However, few studies have investigated these microbes in estuary waters, despite the fact nitrogen concentrations in estuaries are often far higher than the ocean, and can cause drastic ecological harm. We sought to determine the roles of AOA and AOB in driving pelagic nitrification throughout San Francisco Bay, by combining biogeochemical rate measurements with a suite of measurements of the abundance and diversity of AOA and AOB. It addition to traditional functional gene analyses and high-throughput 16S amplicon sequencing, we developed novel qPCR assays to selectively target the ammonia-oxidizing clades found in this estuary, which gave insights into clade-specific distributional patterns. Our biogeochemical data suggest a sizable fraction of ammonium in the bay is oxidized in the water column, likely by AOA, with nitrification in bottom waters also oxidizing a substantial portion of the ammonium exuded by sediments. Generally, Sacramento River waters and Suisun Bay bottom waters had the highest nitrification rates. AOA outnumbered AOB at most stations, and were present in high abundance at both the marine and freshwater ends of the estuary, while AOB abundance was highest in the low-salinity, brackish regions. Different archaeal clades were found at either end of the estuary, suggesting strong niche partitioning along the salinity gradient, with a third clade present largely in brackish waters. This work helps to assess the ability of ammonia-oxidizing microbes in estuaries to transform nitrogen prior to water discharge into the sea, and

  5. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  6. Distinct SagA from Hospital-Associated Clade A1 Enterococcus faecium Strains Contributes to Biofilm Formation

    PubMed Central

    Paganelli, F. L.; de Been, M.; Braat, J. C.; Hoogenboezem, T.; Vink, C.; Bayjanov, J.; Rogers, M. R. C.; Huebner, J.; Bonten, M. J. M.; Willems, R. J. L.

    2015-01-01

    Enterococcus faecium is an important nosocomial pathogen causing biofilm-mediated infections. Elucidation of E. faecium biofilm pathogenesis is pivotal for the development of new strategies to treat these infections. In several bacteria, extracellular DNA (eDNA) and proteins act as matrix components contributing to biofilm development. In this study, we investigated biofilm formation capacity and the roles of eDNA and secreted proteins for 83 E. faecium strains with different phylogenetic origins that clustered in clade A1 and clade B. Although there was no significant difference in biofilm formation between E. faecium strains from these two clades, the addition of DNase I or proteinase K to biofilms demonstrated that eDNA is essential for biofilm formation in most E. faecium strains, whereas proteolysis impacted primarily biofilms of E. faecium clade A1 strains. Secreted antigen A (SagA) was the most abundant protein in biofilms from E. faecium clade A1 and B strains, although its localization differed between the two groups. sagA was present in all sequenced E. faecium strains, with a consistent difference in the repeat region between the clades, which correlated with the susceptibility of biofilms to proteinase K. This indicates an association between the SagA variable repeat profile and the localization and contribution of SagA in E. faecium biofilms. PMID:26209668

  7. Distinct SagA from Hospital-Associated Clade A1 Enterococcus faecium Strains Contributes to Biofilm Formation.

    PubMed

    Paganelli, F L; de Been, M; Braat, J C; Hoogenboezem, T; Vink, C; Bayjanov, J; Rogers, M R C; Huebner, J; Bonten, M J M; Willems, R J L; Leavis, H L

    2015-10-01

    Enterococcus faecium is an important nosocomial pathogen causing biofilm-mediated infections. Elucidation of E. faecium biofilm pathogenesis is pivotal for the development of new strategies to treat these infections. In several bacteria, extracellular DNA (eDNA) and proteins act as matrix components contributing to biofilm development. In this study, we investigated biofilm formation capacity and the roles of eDNA and secreted proteins for 83 E. faecium strains with different phylogenetic origins that clustered in clade A1 and clade B. Although there was no significant difference in biofilm formation between E. faecium strains from these two clades, the addition of DNase I or proteinase K to biofilms demonstrated that eDNA is essential for biofilm formation in most E. faecium strains, whereas proteolysis impacted primarily biofilms of E. faecium clade A1 strains. Secreted antigen A (SagA) was the most abundant protein in biofilms from E. faecium clade A1 and B strains, although its localization differed between the two groups. sagA was present in all sequenced E. faecium strains, with a consistent difference in the repeat region between the clades, which correlated with the susceptibility of biofilms to proteinase K. This indicates an association between the SagA variable repeat profile and the localization and contribution of SagA in E. faecium biofilms. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

    PubMed Central

    Seedorf, Henning; Kittelmann, Sandra

    2014-01-01

    Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ± standard deviation, 89.6% ± 9.8%) and Methanomassiliicoccales (10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ± 6.7%) and Methanosphaera sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens. PMID:25416771

  9. A revision of the Solanum elaeagnifolium clade (Elaeagnifolium clade; subgenus Leptostemonum, Solanaceae)

    PubMed Central

    Knapp, Sandra; Sagona, Eva; Carbonell, Anna K.Z.; Chiarini, Franco

    2017-01-01

    Abstract The Solanum elaeagnifolium clade (Elaeagnifolium clade) contains five species of small, often rhizomatous, shrubs from deserts and dry forests in North and South America. Members of the clade were previously classified in sections Leprophora, Nycterium and Lathyrocarpum, and were not thought to be closely related. The group is sister to the species-rich monophyletic Old World clade of spiny solanums. The species of the group have an amphitropical distribution, with three species in Mexico and the southwestern United States and three species in Argentina. Solanum elaeagnifolium occurs in both North and South America, and is a noxious invasive weed in dry areas worldwide. Members of the group are highly variable morphologically, and this variability has led to much synonymy, particularly in the widespread S. elaeagnifolium. We here review the taxonomic history, morphology, relationships and ecology of these species and provide keys for their identification, descriptions, full synonymy (including designations of lectotypes) and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species. PMID:29033654

  10. Assessing the exoproteome of marine bacteria, lesson from a RTX-toxin abundantly secreted by Phaeobacter strain DSM 17395.

    PubMed

    Durighello, Emie; Christie-Oleza, Joseph Alexander; Armengaud, Jean

    2014-01-01

    Bacteria from the Roseobacter clade are abundant in surface marine ecosystems as over 10% of bacterial cells in the open ocean and 20% in coastal waters belong to this group. In order to document how these marine bacteria interact with their environment, we analyzed the exoproteome of Phaeobacter strain DSM 17395. We grew the strain in marine medium, collected the exoproteome and catalogued its content with high-throughput nanoLC-MS/MS shotgun proteomics. The major component represented 60% of the total protein content but was refractory to either classical proteomic identification or proteogenomics. We de novo sequenced this abundant protein with high-resolution tandem mass spectra which turned out being the 53 kDa RTX-toxin ZP_02147451. It comprised a peptidase M10 serralysin domain. We explained its recalcitrance to trypsin proteolysis and proteomic identification by its unusual low number of basic residues. We found this is a conserved trait in RTX-toxins from Roseobacter strains which probably explains their persistence in the harsh conditions around bacteria. Comprehensive analysis of exoproteomes from environmental bacteria should take into account this proteolytic recalcitrance.

  11. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE - 2014

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  12. Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain.

    PubMed

    Amigo, Natalia; Zhang, Qi; Amadio, Ariel; Zhang, Qunjie; Silva, Wanderson M; Cui, Baiyuan; Chen, Zhongjian; Larzabal, Mariano; Bei, Jinlong; Cataldi, Angel

    2016-01-01

    Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS), and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS) through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6), obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3). Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE), phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.

  13. High abundance and diversity of consumers associated with eutrophic areas in a semi-desert macrotidal coastal ecosystem in Patagonia, Argentina

    NASA Astrophysics Data System (ADS)

    Martinetto, Paulina; Daleo, Pedro; Escapa, Mauricio; Alberti, Juan; Isacch, Juan Pablo; Fanjul, Eugenia; Botto, Florencia; Piriz, Maria Luz; Ponce, Gabriela; Casas, Graciela; Iribarne, Oscar

    2010-07-01

    Here we evaluated the response to eutrophication in terms of abundance and diversity of flora and fauna in a semi-desert macrotidal coastal system (San Antonio bay, Patagonia, Argentina, 40° 48' S) where signs of eutrophication (high nutrient concentration, seaweed blooms, high growth rate of macroalgae) have been reported. We compared abundances and species composition of macroalgae, small infaunal and epifaunal invertebrates, and birds associated with tidal channels of the San Antonio Bay subject to contrasting anthropogenic influence. Macroalgae were more abundant and diverse in the channel closer to human activity where nutrient concentrations were also higher. In contrast to what others have observed in eutrophic sites, small invertebrates and birds were also more abundant and diverse in the channel with macroalgal blooms and high nutrient concentration. The large water flushing during the tidal cycle could prevent anoxic or hypoxic events, making the environment suitable for consumers. Thus, this could be a case in which eutrophication supports high densities of consumers by increasing food availability, rather than negatively affecting the survival of organisms.

  14. Effects of clearcutting with corridor retention on abundance, richness, and diversity of small mammals in the Coastal Plain of South Carolina, USA.

    Treesearch

    Nicole L. Constantine; Tyler A. Campbell; William M. Baughman; Timothy B. Harrington; Brian R. Chapman; Karl V. Miller

    2004-01-01

    We studied six pine plantations in coastal South Carolina to determine the influence of clearcutting with corridor retention on small mammal abundance, richness, and diversity. Small mammals were live-trapped in recently clearcut stands that retained pine corridors 100 m in width and in adjacent pine plantations, 20--23-years-old. We compared small mammal communities...

  15. A comparative study on mesozooplankton abundance and diversity between a protected and an unprotected coastal area of Andaman Islands.

    PubMed

    Pillai, Honey U K; Jayalakshmy, K V; Biju, A; Jayalakshmi, K J; Paulinose, V T; Devi, C B L; Nair, V R; Revichandran, C; Menon, N R; Achuthankutty, C T; Panampunnayil, S U

    2014-06-01

    The study was carried out to understand the variability in phytoplankton production (Chlorophyll a) and mesozooplankton diversity from two different shallow coastal regions of south Andaman viz. Port Blair Bay (PBB), the only real urban area among the islands and Mahatma Gandhi Marine National Park, a Marine Protected Area (MPA) at Wandoor. Seasonal sampling was carried out during the Northeast monsoon (NEM--November 2005), Intermonsoon (IM--April 2006), and Southwest monsoon (SWM--August 2006). Significant (P < 0.05) seasonal variation was observed in the environmental variables at both the regions. Higher average chlorophyll a (Chl. a) and mesozooplankton standing stock were observed at PBB compared to MPA, but the seasonal variation observed was marginal at both the study areas. Chl. a showed a steep increasing gradient from outer to the inner regions of the PBB. The number of zooplankton taxa recorded at both areas was quite similar, but marked differences were noticed in their relative contribution to the total abundance. Eventhough the Copepoda dominated at both the areas, the non-copepod taxa differed significantly between the regions. Dominance of carnivores such as siphonophores and chaetognaths were noticed at PBB, while filter feeders such as appendicularians and decapod larvae were more abundant at MPA. A total of 20 and 21 copepod families was recorded from PBB and MPA, respectively. Eleven species of chaetognaths were observed as common at both areas. Larval decapods were found to be predominant at MPA with 20 families; whereas, at PBB, only 12 families were recorded. In the light of the recent reports on various changes occurring in the coastal waters of the Andaman Islands, it is suspected that the difference in Chl. a as well as the mesozooplankton standing stock and community structure observed between the two study areas may be related to the various anthropogenic events influencing the coastal waters.

  16. Clade perseverance from Mesozoic to present: a multidisciplinary approach to interpretation of pattern and process.

    PubMed

    Barnes, David K A

    2002-10-01

    Two clades of marine bryozoans, cyclostomes and cheilostomes, exemplify the benefits of applying a multidisciplinary approach to the interpretation of long-term evolutionary patterns. The cyclostome bryozoans were dominant in the Mesozoic; since that era, they have decreased in absolute terms and the cheilostomes have come to exceed them in both abundance and diversity. Many studies of living assemblages of the encrusting members of these two clades indicate that cheilostomes are superior space competitors, but paleontological studies suggest that competition between the two taxa has not been escalating over geological time. Both clades occur throughout the world's oceans and seas, and recent work in the geographical extremes has shown that the relative success of the clades varies markedly from place to place. In this study, the importance of differential patterns of recruitment and cumulative space occupation in the two clades was evaluated over four years and in two environments, one temperate and one polar. In both of these environments, peaks of recruitment and space occupation by the two clades were out of phase. The different strategies and outcomes of spatial competition are examined, largely using data from the literature. Only recently has it been realized that tied outcomes of competition are stable alternative results and not simply transitory phases. Many competitive encounters involving cyclostomes result in ties, implying that their strategy is based on persistence rather than dominance. When different indices and models are used to analyze competition data from the two clades, the interpretation varies markedly with methodology. The differences in patterns of recruitment, space occupation, and spatial competition have influenced both our understanding of how the two clades have persisted alongside each other and our perception of cheilostome superiority. Analysis of fluid dynamics has shown that small differences in the mechanical structure of

  17. Diversity and abundance of photosynthetic sponges in temperate Western Australia

    PubMed Central

    Lemloh, Marie-Louise; Fromont, Jane; Brümmer, Franz; Usher, Kayley M

    2009-01-01

    Background Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA) with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. Results We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. Conclusion Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide range of sponges in a wide range

  18. Cranial base evolution within the hominin clade

    PubMed Central

    Nevell, L; Wood, B

    2008-01-01

    The base of the cranium (i.e. the basioccipital, the sphenoid and the temporal bones) is of particular interest because it undergoes significant morphological change within the hominin clade, and because basicranial morphology features in several hominin species diagnoses. We use a parsimony analysis of published cranial and dental data to predict the cranial base morphology expected in the hypothetical last common ancestor of the Pan–Homo clade. We also predict the primitive condition of the cranial base for the hominin clade, and document the evolution of the cranial base within the major subclades within the hominin clade. This analysis suggests that cranial base morphology has continued to evolve in the hominin clade, both before and after the emergence of the genus Homo. PMID:18380865

  19. Assessing the Exoproteome of Marine Bacteria, Lesson from a RTX-Toxin Abundantly Secreted by Phaeobacter Strain DSM 17395

    PubMed Central

    Durighello, Emie; Christie-Oleza, Joseph Alexander; Armengaud, Jean

    2014-01-01

    Bacteria from the Roseobacter clade are abundant in surface marine ecosystems as over 10% of bacterial cells in the open ocean and 20% in coastal waters belong to this group. In order to document how these marine bacteria interact with their environment, we analyzed the exoproteome of Phaeobacter strain DSM 17395. We grew the strain in marine medium, collected the exoproteome and catalogued its content with high-throughput nanoLC-MS/MS shotgun proteomics. The major component represented 60% of the total protein content but was refractory to either classical proteomic identification or proteogenomics. We de novo sequenced this abundant protein with high-resolution tandem mass spectra which turned out being the 53 kDa RTX-toxin ZP_02147451. It comprised a peptidase M10 serralysin domain. We explained its recalcitrance to trypsin proteolysis and proteomic identification by its unusual low number of basic residues. We found this is a conserved trait in RTX-toxins from Roseobacter strains which probably explains their persistence in the harsh conditions around bacteria. Comprehensive analysis of exoproteomes from environmental bacteria should take into account this proteolytic recalcitrance. PMID:24586966

  20. Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico

    USGS Publications Warehouse

    Wawrik, B.; Paul, J.H.; Campbell, L.; Griffin, D.; Houchin, L.; Fuentes-Ortega, A.; Muller-Karger, F.

    2003-01-01

    Low salinity plumes of coastal origin are occasionally found far offshore, where they display a distinct color signature detectable by satellites. The impact of such plumes on carbon fixation and phytoplankton community structure in vertical profiles and on basin wide scales is poorly understood. On a research cruise in June 1999, ocean-color satellite-images (Sea-viewing Wide Field-of-view Sensor, SeaWiFS) were used in locating a Mississippi River plume in the eastern Gulf of Mexico. Profiles sampled within and outside of the plume were analyzed using flow cytometry, HPLC pigment analysis and primary production using 14C incorporation. Additionally, RubisCO large subunit (rbcL) gene expression was measured by hybridization of extracted RNA using 3 full-length RNA gene probes specific for individual phytoplankton clades. We also used a combination of RT-PCR/PCR and TA cloning in order to generate cDNA and DNA rbcL clone libraries from samples taken in the plume. Primary productivity was greatest in the low salinity surface layer of the plume. The plume was also associated with high Synechococcus counts and a strong peak in Form IA rbcL expression. Form IB rbcL (green algal) mRNA was abundant at the subsurface chlorophyll maximum (SCM), whereas Form ID rbcL (chromophytic) expression showed little vertical structure. Phylogenetic analysis of cDNA libraries demonstrated the presence of Form IA rbcL Synechococcus phylotypes in the plume. Below the plume, 2 spatially separated and genetically distinct rbcL clades of Prochlorococcus were observed. This indicated the presence of the high- and low-light adapted clades of Prochlorococcus. A large and very diverse clade of Prymnesiophytes was distributed throughout the water column, whereas a clade of closely related prasinophytes may have dominated at the SCM. These data indicate that the Mississippi river plume may dramatically alter the surface picoplankton composition of the Gulf of Mexico, with Synechococcus displacing

  1. What limits the morphological disparity of clades?

    PubMed Central

    Oyston, Jack W.; Hughes, Martin; Wagner, Peter J.; Gerber, Sylvain; Wills, Matthew A.

    2015-01-01

    The morphological disparity of species within major clades shows a variety of trajectory patterns through evolutionary time. However, there is a significant tendency for groups to reach their maximum disparity relatively early in their histories, even while their species richness or diversity is comparatively low. This pattern of early high-disparity suggests that there are internal constraints (e.g. developmental pleiotropy) or external restrictions (e.g. ecological competition) upon the variety of morphologies that can subsequently evolve. It has also been demonstrated that the rate of evolution of new character states decreases in most clades through time (character saturation), as does the rate of origination of novel bodyplans and higher taxa. Here, we tested whether there was a simple relationship between the level or rate of character state exhaustion and the shape of a clade's disparity profile: specifically, its centre of gravity (CG). In a sample of 93 extinct major clades, most showed some degree of exhaustion, but all continued to evolve new states up until their extinction. Projection of states/steps curves suggested that clades realized an average of 60% of their inferred maximum numbers of states. Despite a weak but significant correlation between overall levels of homoplasy and the CG of clade disparity profiles, there were no significant relationships between any of our indices of exhaustion curve shape and the clade disparity CG. Clades showing early high-disparity were no more likely to have early character saturation than those with maximum disparity late in their evolution. PMID:26640649

  2. The “χ” of the Matter: Testing the Relationship between Paleoenvironments and Three Theropod Clades

    PubMed Central

    Sales, Marcos A. F.; Lacerda, Marcel B.; Horn, Bruno L. D.; de Oliveira, Isabel A. P.; Schultz, Cesar L.

    2016-01-01

    The view of spinosaurs as dinosaurs of semi-aquatic habits and strongly associated with marginal and coastal habitats are deeply rooted in both scientific and popular knowledge, but it was never statistically tested. Inspired by a previous analysis of other dinosaur clades and major paleoenvironmental categories, here we present our own statistical evaluation of the association between coastal and terrestrial paleoenvironments and spinosaurids, along with other two theropod taxa: abelisaurids and carcharodontosaurids. We also included a taphonomic perspective and classified the occurrences in categories related to potential biases in order to better address our interpretations. Our main results can be summarized as follows: 1) the taxon with the largest amount of statistical evidence showing it positively associated to coastal paleoenvironments is Spinosauridae; 2) abelisaurids and carcharodontosaurids had more statistical evidence showing them positively associated with terrestrial paleoenvironments; 3) it is likely that spinosaurids also occupied spatially inland areas in a way somehow comparable at least to carcharodontosaurids; 4) abelisaurids may have been more common than the other two taxa in inland habitats. PMID:26829315

  3. Seasonal abundance and vertical distribution of capelin (Mallotus villosus) in relation to water temperature at a coastal site off eastern Newfoundland

    USGS Publications Warehouse

    Methven, David A.; Piatt, John F.

    1991-01-01

    The seasonal abundance and vertical distribution of capelin in relation to water temperature have been investigated by conducting repeated hydroacoustic surveys at a coastal site off eastern Newfoundland. Water temperatures were warmer in 1983 than in 1984 as indicated by the earlier appearance and greater depth of the seasonal thermocline. Correspondingly, schools of capelin appeared earlier, were more abundant, and extended deeper in the water column in 1983 than in 1984. Most capelin were found between the surface and the 5°C isotherm. In both years, initial peaks of capelin abundance occurred when nearshore water temperatures increased from about 0-1°C to above 6°C and, at or near, periods of maximum tidal oscillation. Short-term variations in the depth of the 5°C isotherm were related to nearshore wind-induced upwelling events. Annual variations corresponded to the volume of cold (>0°C) water and sea-ice transported south by the Labrador Current.

  4. Evidence of Sympatry of Clade A and Clade B Head Lice in a Pre-Columbian Chilean Mummy from Camarones

    PubMed Central

    Boutellis, Amina; Drali, Rezak; Rivera, Mario A.; Mumcuoglu, Kosta Y.; Raoult, Didier

    2013-01-01

    Three different lineages of head lice are known to parasitize humans. Clade A, which is currently worldwide in distribution, was previously demonstrated to be present in the Americas before the time of Columbus. The two other types of head lice are geographically restricted to America and Australia for clade B and to Africa and Asia for clade C. In this study, we tested two operculated nits from a 4,000-year-old Chilean mummy of Camarones for the presence of the partial Cytb mitochondrial gene (270 bp). Our finding shows that clade B head lice were present in America before the arrival of the European colonists. PMID:24204678

  5. Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.

    PubMed

    Bass, David; Tikhonenkov, Denis Victorovich; Foster, Rachel; Dyal, Patricia; Janouškovec, Jan; Keeling, Patrick J; Gardner, Michelle; Neuhauser, Sigrid; Hartikainen, Hanna; Mylnikov, Alexandre P; Berney, Cédric

    2018-04-15

    Rhizarian 'Novel Clade 10' (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp. and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, here named Aquavolonida ord. nov. The slightly metabolic cells possess naked heterodynamic flagella, whose kinetosomes lie at a right angle to each other and are connected by at least one fibril. Unlike their closest known relative Tremula longifila, they rotate around their longitudinal axis when swimming and only very rarely glide on surfaces. Screening of a wide range of environmental DNA extractions with lineage-specific PCR primers reveals that Aquavolonida consists of a large radiation of protists, which are most diversified in freshwater planktonic habitats and as yet undetected in marine environments. Earlier-branching lineages in Aquavolonida include less frequently detected organisms from soils and freshwater sediments. The 18S rRNA gene phylogeny suggests that Aquavolonida forms a common evolutionary lineage with tremulids and uncharacterized 'Novel Clade 12', which likely represents one of the deepest lineages in the Rhizaria, separate from Cercozoa (Filosa), Endomyxa, and Retaria. © 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

  6. Spatiotemporal patterns of phytoplankton composition and abundance in the Maryland Coastal Bays: The influence of freshwater discharge and anthropogenic activities

    NASA Astrophysics Data System (ADS)

    Oseji, Ozuem F.; Chigbu, Paulinus; Oghenekaro, Efeturi; Waguespack, Yan; Chen, Nianhong

    2018-07-01

    The spatial and temporal variations in phytoplankton abundance and community structure in the northern and southern parts of the Maryland Coastal Bays (MCBs) that differ in anthropogenic activities and hydrological characteristics were studied in 2012 and 2013 using photosynthetic pigments as biomarkers. Phytoplankton pigment biomass and diversity were generally higher in the northern bays that receive high nutrient input from St. Martin River, than in the southern bays where nutrient levels were comparatively low. Sites close to the mouths of tributaries in northern and southern bays had higher nutrient levels, which favored the development of dinoflagellates, and nano- and picophytoplankton, than sites closer to the inlets. The microplankton dominated the phytoplankton community in spring (>90%) and decreased in relative abundance into fall (<60%) whereas nanoplankton peaked in summer or fall. Picoplankton relative abundance increased from late spring (<10%, March 2012 & 2013) to summer (40%, July 2012 and August 2013) and was correlated positively with NH4+ and negatively with salinity. The observed spatial and seasonal patterns of phytoplankton relative abundance and diversity are likely due to changes in nutrient concentrations and ratios, driven by variations in freshwater discharge, and selective grazing of phytoplankton. Water quality management in the MCBs should continue to focus on reducing nutrient inputs into the bays.

  7. Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass

    NASA Astrophysics Data System (ADS)

    Caron, David A.; Connell, Paige E.; Schaffner, Rebecca A.; Schnetzer, Astrid; Fuhrman, Jed A.; Countway, Peter D.; Kim, Diane Y.

    2017-03-01

    Biogeochemistry in marine plankton communities is strongly influenced by the activities of microbial species. Understanding the composition and dynamics of these assemblages is essential for modeling emergent community-level processes, yet few studies have examined all of the biological assemblages present in the plankton, and benchmark data of this sort from time-series studies are rare. Abundance and biomass of the entire microbial assemblage and mesozooplankton (>200 μm) were determined vertically, monthly and seasonally over a 3-year period at a coastal time-series station in the San Pedro Basin off the southwestern coast of the USA. All compartments of the planktonic community were enumerated (viruses in the femtoplankton size range [0.02-0.2 μm], bacteria + archaea and cyanobacteria in the picoplankton size range [0.2-2.0 μm], phototrophic and heterotrophic protists in the nanoplanktonic [2-20 μm] and microplanktonic [20-200 μm] size ranges, and mesozooplankton [>200 μm]. Carbon biomass of each category was estimated using standard conversion factors. Plankton abundances varied over seven orders of magnitude across all categories, and total carbon biomass averaged approximately 60 μg C l-1 in surface waters of the 890 m water column over the study period. Bacteria + archaea comprised the single largest component of biomass (>1/3 of the total), with the sum of phototrophic protistan biomass making up a similar proportion. Temporal variability at this subtropical station was not dramatic. Monthly depth-specific and depth-integrated biomass varied 2-fold at the station, while seasonal variances were generally <50%. This study provides benchmark information for investigating long-term environmental forcing on the composition and dynamics of the microbes that dominate food web structure and function at this coastal observatory.

  8. Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China

    PubMed Central

    Wang, Shaojun; Chen, Han Y. H.; Tan, Yan; Fan, Huan; Ruan, Honghua

    2016-01-01

    Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon’s and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability. PMID:26857390

  9. Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China.

    PubMed

    Wang, Shaojun; Chen, Han Y H; Tan, Yan; Fan, Huan; Ruan, Honghua

    2016-02-09

    Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon's and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability.

  10. Incorporation of Glucose under Anoxic Conditions by Bacterioplankton from Coastal North Sea Surface Waters

    PubMed Central

    Alonso, Cecilia; Pernthaler, Jakob

    2005-01-01

    It has been hypothesized that the potential for anaerobic metabolism might be a common feature of bacteria in coastal marine waters (L. Riemann and F. Azam, Appl. Environ. Microbiol. 68: 5554-5562, 2002). Therefore, we investigated whether different phylogenetic groups of heterotrophic picoplankton from the coastal North Sea were able to take up a simple carbon source under anoxic conditions. Oxic and anoxic incubations (4 h) or enrichments (24 h) of seawater with radiolabeled glucose were performed in July and August 2003. Bacteria with incorporated substrate were identified by using a novel protocol in which we combined fluorescence in situ hybridization and microautoradiography of cells on membrane filters. Incorporation of glucose under oxic and anoxic conditions was found in α-Proteobacteria, γ-Proteobacteria, and the Cytophaga-Flavobacterium cluster of the Bacteroidetes at both times, but not in marine Euryarchaeota. In July, the majority of cells belonging to the α-proteobacterial Roseobacter clade showed tracer incorporation both in oxic incubations and in oxic and anoxic enrichments. In August, only a minority of the Roseobacter cells, but most bacteria affiliated with Vibrio spp., were able to incorporate the tracer under either condition. A preference for glucose uptake under anoxic conditions was observed for bacteria related to Alteromonas and the Pseudoalteromonas-Colwellia group. These genera are commonly considered to be strictly aerobic, but facultatively fermentative strains have been described. Our findings suggest that the ability to incorporate substrates anaerobically is widespread in pelagic marine bacteria belonging to different phylogenetic groups. Such bacteria may be abundant in fully aerated coastal marine surface waters. PMID:15811993

  11. Differential Penicillin-Binding Protein 5 (PBP5) Levels in the Enterococcus faecium Clades with Different Levels of Ampicillin Resistance.

    PubMed

    Montealegre, Maria Camila; Roh, Jung Hyeob; Rae, Meredith; Davlieva, Milya G; Singh, Kavindra V; Shamoo, Yousif; Murray, Barbara E

    2017-01-01

    Ampicillin resistance in Enterococcus faecium is a serious concern worldwide, complicating the treatment of E. faecium infections. Penicillin-binding protein 5 (PBP5) is considered the main ampicillin resistance determinant in E. faecium The three known E. faecium clades showed sequence variations in the pbp5 gene that are associated with their ampicillin resistance phenotype; however, these changes alone do not explain the array of resistance levels observed among E. faecium clinical strains. We aimed to determine if the levels of PBP5 are differentially regulated between the E. faecium clades, with the hypothesis that variations in PBP5 levels could help account for the spectrum of ampicillin MICs seen in E. faecium We studied pbp5 mRNA levels and PBP5 protein levels as well as the genetic environment upstream of pbp5 in 16 E. faecium strains that belong to the different E. faecium clades and for which the ampicillin MICs covered a wide range. Our results found that pbp5 and PBP5 levels are increased in subclade A1 and A2 ampicillin-resistant strains compared to those in clade B and subclade A2 ampicillin-susceptible strains. Furthermore, we found evidence of major clade-associated rearrangements in the region upstream of pbp5, including large DNA fragment insertions, deletions, and single nucleotide polymorphisms, that may be associated with the differential regulation of PBP5 levels between the E. faecium clades. Overall, these findings highlight the contribution of the clade background to the regulation of PBP5 abundance and point to differences in the region upstream of pbp5 as likely contributors to the differential expression of ampicillin resistance. Copyright © 2016 American Society for Microbiology.

  12. Spatial and temporal variability in coccolithophore abundance and distribution in the NW Iberian coastal upwelling system

    NASA Astrophysics Data System (ADS)

    Ausín, Blanca; Zúñiga, Diana; Flores, Jose A.; Cavaleiro, Catarina; Froján, María; Villacieros-Robineau, Nicolás; Alonso-Pérez, Fernando; Arbones, Belén; Santos, Celia; de la Granda, Francisco; Castro, Carmen G.; Abrantes, Fátima; Eglinton, Timothy I.; Salgueiro, Emilia

    2018-01-01

    A systematic investigation of the spatial and temporal variability in coccolithophore abundance and distribution through the water column of the NW Iberian coastal upwelling system was performed. From July 2011 to June 2012, monthly sampling at various water depths was conducted at two parallel stations located at 42° N. Total coccosphere abundance was higher at the outer-shelf station, where warmer, nutrient-depleted waters favoured coccolithophore rather than phytoplanktonic diatom blooms, which are known to dominate the inner-shelf location. In seasonal terms, higher coccosphere and coccolith abundances were registered at both stations during upwelling seasons, coinciding with high irradiance levels. This was typically in conjunction with stratified, nutrient-poor conditions (i.e. relaxing upwelling conditions). However, it also occurred during some upwelling events of colder, nutrient-rich subsurface waters onto the continental shelf. Minimum abundances were generally found during downwelling periods, with unexpectedly high coccolith abundance registered in subsurface waters at the inner-shelf station. This finding can only be explained if strong storms during these downwelling periods favoured resuspension processes, thus remobilizing deposited coccoliths from surface sediments, and hence hampering the identification of autochthonous coccolithophore community structure. At both locations, the major coccolithophore assemblages were dominated by Emiliania huxleyi, small Gephyrocapsa group, Gephyrocapsa oceanica, Florisphaera profunda, Syracosphaera spp., Coronosphaera mediterranea, and Calcidiscus leptoporus. Ecological preferences of the different taxa were assessed by exploring the relationships between environmental conditions and temporal and vertical variability in coccosphere abundance. These findings provide relevant information for the use of fossil coccolith assemblages in marine sediment records, in order to infer past environmental conditions, of

  13. Breadth of neutralizing antibodies elicited by stable, homogeneous clade A and clade C HIV-1 gp140 envelope trimers in guinea pigs.

    PubMed

    Nkolola, Joseph P; Peng, Hanqin; Settembre, Ethan C; Freeman, Michael; Grandpre, Lauren E; Devoy, Colleen; Lynch, Diana M; La Porte, Annalena; Simmons, Nathaniel L; Bradley, Ritu; Montefiori, David C; Seaman, Michael S; Chen, Bing; Barouch, Dan H

    2010-04-01

    The native envelope (Env) spike on the surface of human immunodeficiency virus type 1 (HIV-1) is trimeric, and thus trimeric Env vaccine immunogens are currently being explored in preclinical immunogenicity studies. Key challenges have included the production and purification of biochemically homogeneous and stable trimers and the evaluation of these immunogens utilizing standardized virus panels for neutralization assays. Here we report the binding and neutralizing antibody (NAb) responses elicited by clade A (92UG037.8) and clade C (CZA97.012) Env gp140 trimer immunogens in guinea pigs. These trimers have been selected and engineered for optimal biochemical stability and have defined antigenic properties. Purified gp140 trimers with Ribi adjuvant elicited potent, cross-clade NAb responses against tier 1 viruses as well as detectable but low-titer NAb responses against select tier 2 viruses from clades A, B, and C. In particular, the clade C trimer elicited NAbs that neutralized 27%, 20%, and 47% of tier 2 viruses from clades A, B, and C, respectively. Heterologous DNA prime, protein boost as well as DNA prime, recombinant adenovirus boost regimens expressing these antigens, however, did not result in an increased magnitude or breadth of NAb responses in this system. These data demonstrate the immunogenicity of stable, homogeneous clade A and clade C gp140 trimers and exemplify the utility of standardized tier 1 and tier 2 virus panels for assessing the NAb responses of candidate HIV-1 Env immunogens.

  14. Vegetation types in coastal Louisiana in 2013

    USGS Publications Warehouse

    Sasser, Charles E.; Visser, Jenneke M.; Mouton, Edmond; Linscombe, Jeb; Hartley, Steve B.

    2014-01-01

    During the summer of 2013, the U.S. Geological Survey, Louisiana State University, University of Louisiana at Lafayette, and the Louisiana Department of Wildlife and Fisheries Coastal and Nongame Resources Division jointly completed an aerial survey to collect data on 2013 vegetation types in coastal Louisiana. Plant species were listed and their abundance classified. On the basis of species composition and abundance, each marsh sampling station was assigned a marsh type: fresh, intermediate, brackish, or saline (saltwater) marsh. The current map presents the data collected in this effort.

  15. Gastrointestinal Tract Colonization Dynamics by Different Enterococcus faecium Clades

    PubMed Central

    Montealegre, Maria Camila; Singh, Kavindra V.; Murray, Barbara E.

    2016-01-01

    Colonization of the gastrointestinal tract (GIT) generally precedes infection with antibiotic-resistant Enterococcus faecium. We used a mouse GIT colonization model to test differences in the colonization levels by strains from different E. faecium lineages: clade B, part of the healthy human microbiota; subclade A1, associated with infections; and subclade A2, primarily associated with animals. After mono-inoculation, there was no significant difference in colonization (measured as the geometric mean number of colony-forming units per gram) by the E. faecium clades at any time point (P > .05). However, in competition assays, with 6 of the 7 pairs, clade B strains outcompeted clade A strains in their ability to persist in the GIT; this difference was significant in some pairs by day 2 and in all pairs by day 14 (P < .0008–.0283). This observation may explain the predominance of clade B in the community and why antibiotic-resistant hospital-associated E. faecium are often replaced by clade B strains once patients leave the hospital. PMID:26671890

  16. Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change.

    PubMed

    Evans, Claire; Brandsma, Joost; Pond, David W; Venables, Hugh J; Meredith, Michael P; Witte, Harry J; Stammerjohn, Sharon; Wilson, William H; Clarke, Andrew; Brussaard, Corina P D

    2017-02-01

    An 8-year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. The hominin fossil record: taxa, grades and clades

    PubMed Central

    Wood, Bernard; Lonergan, Nicholas

    2008-01-01

    This paper begins by reviewing the fossil evidence for human evolution. It presents summaries of each of the taxa recognized in a relatively speciose hominin taxonomy. These taxa are grouped in grades, namely possible and probable hominins, archaic hominins, megadont archaic hominins, transitional hominins, pre-modern Homo and anatomically modern Homo. The second part of this contribution considers some of the controversies that surround hominin taxonomy and systematics. The first is the vexed question of how you tell an early hominin from an early panin, or from taxa belonging to an extinct clade closely related to the Pan-Homo clade. Secondly, we consider how many species should be recognized within the hominin fossil record, and review the philosophies and methods used to identify taxa within the hominin fossil record. Thirdly, we examine how relationships within the hominin clade are investigated, including descriptions of the methods used to break down an integrated structure into tractable analytical units, and then how cladograms are generated and compared. We then review the internal structure of the hominin clade, including the problem of how many subclades should be recognized within the hominin clade, and we examine the reliability of hominin cladistic hypotheses. The last part of the paper reviews the concepts of a genus, including the criteria that should be used for recognizing genera within the hominin clade. PMID:18380861

  18. Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments.

    PubMed

    Chen, Jing; Gu, Ji-Dong

    2017-07-01

    In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH 4 + but lower concentrations of both NO 2 - and NO 3 - , and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH 4 + and NO 2 - were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

  19. Symbiodinium Clade Affects Coral Skeletal Isotopic Ratio

    NASA Astrophysics Data System (ADS)

    Carilli, J.; Charles, C. D.; Garren, M.; McField, M.; Norris, R. D.

    2011-12-01

    The influence of different physiologies of Symbiodinium dinoflagellate symbiont clades on the skeletal chemistry of associated coral hosts has not previously been investigated. This is an important issue because coral skeletons are routinely used for tropical paleoclimatic reconstructions. We analyzed coral skeletal samples collected simultaneously from neighboring colonies off Belize and found that those harboring different clades of Symbiodinium displayed significantly different skeletal oxygen isotopic compositions. We also found evidence for mean shifts in skeletal oxygen isotopic composition after coral bleaching (the loss and potential exchange of symbionts) in two of four longer coral cores from the Mesoamerican Reef, though all experienced similar climatic conditions. Thus, we suggest that symbiont clade identity leaves a signature in the coral skeletal archive and that this influence must be considered for quantitative environmental reconstruction. In addition, we suggest that the skeletal isotopic signature may be used to identify changes in the dominant symbiont clade that have occurred in the past, to identify how common and widespread this phenomenon is--a potential adaptation to climate change.

  20. Gastrointestinal Tract Colonization Dynamics by Different Enterococcus faecium Clades.

    PubMed

    Montealegre, Maria Camila; Singh, Kavindra V; Murray, Barbara E

    2016-06-15

    Colonization of the gastrointestinal tract (GIT) generally precedes infection with antibiotic-resistant Enterococcus faecium We used a mouse GIT colonization model to test differences in the colonization levels by strains from different E. faecium lineages: clade B, part of the healthy human microbiota; subclade A1, associated with infections; and subclade A2, primarily associated with animals. After mono-inoculation, there was no significant difference in colonization (measured as the geometric mean number of colony-forming units per gram) by the E. faecium clades at any time point (P > .05). However, in competition assays, with 6 of the 7 pairs, clade B strains outcompeted clade A strains in their ability to persist in the GIT; this difference was significant in some pairs by day 2 and in all pairs by day 14 (P < .0008-.0283). This observation may explain the predominance of clade B in the community and why antibiotic-resistant hospital-associated E. faecium are often replaced by clade B strains once patients leave the hospital. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  1. COASTAL INVERTEBRATES AND FISHES: HOW WILL THEY BE AFFECTED BY CHANGING ENVIRONMENTAL CONDITIONS- INCORPORATING CLIMATE SCENARIOS INTO THE COASTAL BIODIVERSITY RISK ANALYSIS TOOL (CBRAT)

    EPA Science Inventory

    The Coastal Biodiversity Risk Analysis Tool (CBRAT) is a public website that functions as an ecoinformatics platform to synthesize biogeographical distributions, abundances, life history attributes, and environmental tolerances for near-coastal invertebrates and fishes on a broad...

  2. Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya.

    PubMed

    Kiyuka, Patience K; Agoti, Charles N; Munywoki, Patrick K; Njeru, Regina; Bett, Anne; Otieno, James R; Otieno, Grieven P; Kamau, Everlyn; Clark, Taane G; van der Hoek, Lia; Kellam, Paul; Nokes, D James; Cotten, Matthew

    2018-05-05

    Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.

  3. Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 from Cattle in Argentina have Hypervirulent-Like Phenotypes

    PubMed Central

    Amigo, Natalia; Mercado, Elsa; Bentancor, Adriana; Singh, Pallavi; Vilte, Daniel; Gerhardt, Elisabeth; Zotta, Elsa; Ibarra, Cristina; Manning, Shannon D.; Larzábal, Mariano; Cataldi, Angel

    2015-01-01

    The hemolytic uremic syndrome (HUS) whose main causative agent is enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a disease that mainly affects children under 5 years of age. Argentina is the country with the highest incidence of HUS in the world. Cattle are a major reservoir and source of infection with E. coli O157:H7. To date, the epidemiological factors that contribute to its prevalence are poorly understood. Single nucleotide polymorphism (SNP) typing has helped to define nine E. coli O157:H7 clades and the clade 8 strains were associated with most of the cases of severe disease. In this study, eight randomly selected isolates of EHEC O157:H7 from cattle in Argentina were studied as well as two human isolates. Four of them were classified as clade 8 through the screening for 23 SNPs; the two human isolates grouped in this clade as well, while two strains were closely related to strains representing clade 6. To assess the pathogenicity of these strains, we assayed correlates of virulence. Shiga toxin production was determined by an ELISA kit. Four strains were high producers and one of these strains that belonged to a novel genotype showed high verocytotoxic activity in cultured cells. Also, these clade 8 and 6 strains showed high RBC lysis and adherence to epithelial cells. One of the clade 6 strains showed stronger inhibition of normal water absorption than E. coli O157:H7 EDL933 in human colonic explants. In addition, two of the strains showing high levels of Stx2 production and RBC lysis activity were associated with lethality and uremia in a mouse model. Consequently, circulation of such strains in cattle may partially contribute to the high incidence of HUS in Argentina. PMID:26030198

  4. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

    PubMed

    Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

    2017-01-01

    Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  5. Clades reach highest morphological disparity early in their evolution

    PubMed Central

    Hughes, Martin; Gerber, Sylvain; Wills, Matthew Albion

    2013-01-01

    There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing. PMID:23884651

  6. Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system.

    PubMed

    Christaki, Urania; Kormas, Konstantinos A; Genitsaris, Savvas; Georges, Clément; Sime-Ngando, Télesphore; Viscogliosi, Eric; Monchy, Sébastien

    2014-01-01

    The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.

  7. Tracking Cholera in Coastal Regions using Satellite Observations

    PubMed Central

    Jutla, Antarpreet S; Akanda, Ali S; Islam, Shafiqul

    2010-01-01

    Cholera remains a significant health threat across the globe. The pattern and magnitude of the seven global pandemics suggest that cholera outbreaks primarily originate in coastal regions and then spread inland through secondary means. Cholera bacteria show strong association with plankton abundance in coastal ecosystems. This review study investigates relationship(s) between cholera incidence and coastal processes and explores utility of using remote sensing data to track coastal plankton blooms, using chlorophyll as a surrogate variable for plankton abundance, and subsequent cholera outbreaks. Most studies over the last several decades have primarily focused on the microbiological and epidemiological understanding of cholera outbreaks. Accurate identification and mechanistic understanding of large scale climatic, geophysical and oceanic processes governing cholera-chlorophyll relationship is important for developing cholera prediction models. Development of a holistic understanding of these processes requires long and reliable chlorophyll dataset(s), which are beginning to be available through satellites. We have presented a schematic pathway and a modeling framework that relate cholera with various hydroclimatic and oceanic variables for understanding disease dynamics using latest advances in remote sensing. Satellite data, with its unprecedented spatial and temporal coverage, have potentials to monitor coastal processes and track cholera outbreaks in endemic regions. PMID:21072249

  8. Temporal variability and phylogenetic characterization of planktonic anammox bacteria in the coastal upwelling ecosystem off central Chile

    NASA Astrophysics Data System (ADS)

    Galán, Alexander; Molina, Verónica; Belmar, Lucy; Ulloa, Osvaldo

    2012-01-01

    The phylogenetic affiliation and temporal variability in the abundance of planktonic anammox bacteria were studied at a time-series station above the continental shelf off central Chile (∼36°S; bottom depth 93 m), a wind-driven, seasonal upwelling area, between August 2006 and April 2008. The study was carried out by cloning and sequencing the 16S rRNA gene and by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Our results showed the presence of a single anammox bacteria-like ribotype during both upwelling and non-upwelling seasons, which was phylogenetically associated with a recently described oxygen-minimum-zone subcluster within the Candidatus Scalindua clade. Moreover, clear differences were observed in the temporal and vertical distribution of anammox cells. During the upwelling season (austral spring-summer), relatively high abundances (∼5500 cells mL -1) and large cells (0.8 μm 3-75.7 fg C cell -1) were found below 20 m depth. In contrast, during the non-upwelling season (austral fall-winter), lower abundances (∼600 cells mL -1) and smaller cells (0.1 μm 3-22.8 fg C cell -1) were found, predominantly associated with the bottom layer. Overall, our results indicate that the abundance and vertical distribution of anammox planktonic assemblages are related to the occurrence of seasonal, wind-driven, coastal upwelling, which in turn appears to offer favorable conditions for the development of these microorganisms. The dominance of a unique anammox bacteria-like ribotype could be related to the high environmental variability observed in the system, which prevents the establishment of other anammox lineages.

  9. Combining abundance and performance data reveals how temperature regulates coastal occurrences and activity of a roaming apex predator.

    PubMed

    Payne, Nicholas L; Meyer, Carl G; Smith, James A; Houghton, Jonathan D R; Barnett, Adam; Holmes, Bonnie J; Nakamura, Itsumi; Papastamatiou, Yannis P; Royer, Mark A; Coffey, Daniel M; Anderson, James M; Hutchinson, Melanie R; Sato, Katsufumi; Halsey, Lewis G

    2018-05-01

    The redistribution of species has emerged as one of the most pervasive impacts of anthropogenic climate warming, and presents many societal challenges. Understanding how temperature regulates species distributions is particularly important for mobile marine fauna such as sharks given their seemingly rapid responses to warming, and the socio-political implications of human encounters with some dangerous species. The predictability of species distributions can potentially be improved by accounting for temperature's influence on performance, an elusive relationship for most large animals. We combined multi-decadal catch data and bio-logging to show that coastal abundance and swimming performance of tiger sharks Galeocerdo cuvier are both highest at ~22°C, suggesting thermal constraints on performance may regulate this species' distribution. Tiger sharks are responsible for a large proportion of shark bites on humans, and a focus of controversial control measures in several countries. The combination of distribution and performance data moves towards a mechanistic understanding of tiger shark's thermal niche, and delivers a simple yet powerful indicator for predicting the location and timing of their occurrences throughout coastlines. For example, tiger sharks are mostly caught at Australia's popular New South Wales beaches (i.e. near Sydney) in the warmest months, but our data suggest similar abundances will occur in winter and summer if annual sea surface temperatures increase by a further 1-2°C. © 2018 John Wiley & Sons Ltd.

  10. A comparison of weed communities of coastal rice fields in Peninsular Malaysia.

    PubMed

    Hakim, M A; Juraimi, Abdul Shukor; Hanafi, M M; Selamat, A

    2013-09-01

    A survey was conducted at 100 different rice fields in coastal areas of West Malaysia to identify most common and prevalent weeds associated with rice. Fields surveyed were done according to the quantitative survey method by using 0.5m x 0.5m size quadrate with 20 samples from each field. A total of 53 different weed species belong to 18 families were identified of which 32 annual and 21 perennial; 12 grassy, 13 sedges and 28 broadleaved weeds. Based on relative abundance the most prevalent and abundant weed species were selected in the coastal rice field. Among the 10 most abundant weed species, there were four grasses viz. Echinochloa crusgalli, Leptochloo chinensis, Echinochloo colona, Oryza sotivo L. (weedy rice).; four sedges viz. Fimbristylis miliacea, Cyperus iria, Cyperus difformis, Scirpus grossus and two broadleaved weeds viz. Sphenocleo zeylonica, Jussiaea linifolio. Leptochloa chinensis, E. crusgalli, F. miliocea, E. colona were more prevalent and abundant species out of the 10 most dominant weed species in the coastal rice field of Peninsular Malaysia.

  11. Persistent differences between coastal and offshore kelp forest communities in a warming Gulf of Maine

    PubMed Central

    Lamb, Robert W.

    2018-01-01

    Kelp forests provide important ecosystem services, yet coastal kelp communities are increasingly altered by anthropogenic impacts. Kelp forests in remote, offshore locations may provide an informative contrast due to reduced impacts from local stressors. We tested the hypothesis that shallow kelp assemblages (12–15 m depth) and associated fish and benthic communities in the coastal southwest Gulf of Maine (GOM) differed significantly from sites on Cashes Ledge, 145 km offshore by sampling five coastal and three offshore sites at 43.0 +/- 0.07° N latitude. Offshore sites on Cashes Ledge supported the greatest density (47.8 plants m2) and standing crop biomass (5.5 kg m2 fresh weight) of the foundation species Saccharina latissima kelp at this depth in the Western North Atlantic. Offshore densities of S. latissima were over 150 times greater than at coastal sites, with similar but lower magnitude trends for congeneric S. digitata. Despite these differences, S. latissima underwent a significant 36.2% decrease between 1987 and 2015 on Cashes Ledge, concurrent with a rapid warming of the GOM and invasion by the kelp-encrusting bryozoan Membranipora membranacea. In contrast to kelp, the invasive red alga Dasysiphonia japonica was significantly more abundant at coastal sites, suggesting light or dispersal limitation offshore. Spatial differences in fish abundance mirrored those of kelp, as the average biomass of all fish on Cashes Ledge was 305 times greater than at the coastal sites. Remote video censuses of cod (Gadus morhua), cunner (Tautaogolabrus adspersus), and pollock (Pollachius virens) corroborated these findings. Understory benthic communities also differed between regions, with greater abundance of sessile invertebrates offshore. Populations of kelp-consuming sea urchins Stronglyocentrotus droebachiensis, were virtually absent from Cashes Ledge while small urchins were abundant onshore, suggesting recruitment limitation offshore. Despite widespread warming

  12. Persistent differences between coastal and offshore kelp forest communities in a warming Gulf of Maine.

    PubMed

    Witman, Jon D; Lamb, Robert W

    2018-01-01

    Kelp forests provide important ecosystem services, yet coastal kelp communities are increasingly altered by anthropogenic impacts. Kelp forests in remote, offshore locations may provide an informative contrast due to reduced impacts from local stressors. We tested the hypothesis that shallow kelp assemblages (12-15 m depth) and associated fish and benthic communities in the coastal southwest Gulf of Maine (GOM) differed significantly from sites on Cashes Ledge, 145 km offshore by sampling five coastal and three offshore sites at 43.0 +/- 0.07° N latitude. Offshore sites on Cashes Ledge supported the greatest density (47.8 plants m2) and standing crop biomass (5.5 kg m2 fresh weight) of the foundation species Saccharina latissima kelp at this depth in the Western North Atlantic. Offshore densities of S. latissima were over 150 times greater than at coastal sites, with similar but lower magnitude trends for congeneric S. digitata. Despite these differences, S. latissima underwent a significant 36.2% decrease between 1987 and 2015 on Cashes Ledge, concurrent with a rapid warming of the GOM and invasion by the kelp-encrusting bryozoan Membranipora membranacea. In contrast to kelp, the invasive red alga Dasysiphonia japonica was significantly more abundant at coastal sites, suggesting light or dispersal limitation offshore. Spatial differences in fish abundance mirrored those of kelp, as the average biomass of all fish on Cashes Ledge was 305 times greater than at the coastal sites. Remote video censuses of cod (Gadus morhua), cunner (Tautaogolabrus adspersus), and pollock (Pollachius virens) corroborated these findings. Understory benthic communities also differed between regions, with greater abundance of sessile invertebrates offshore. Populations of kelp-consuming sea urchins Stronglyocentrotus droebachiensis, were virtually absent from Cashes Ledge while small urchins were abundant onshore, suggesting recruitment limitation offshore. Despite widespread warming of

  13. Distribution of mesopredatory fish determined by habitat variables in a predator-depleted coastal system.

    PubMed

    Bergström, Lena; Karlsson, Martin; Bergström, Ulf; Pihl, Leif; Kraufvelin, Patrik

    Shallow nearshore habitats are highly valued for supporting marine ecosystems, but are subject to intense human-induced pressures. Mesopredatory fish are key components in coastal food webs, and alterations in their abundance may have evident effects also on other parts of the ecosystem. The aim of this study was to clarify the relationship between the abundance of coastal mesopredatory fish, defined as mid-trophic level demersal and benthic species with a diet consisting predominantly of invertebrates, and ambient environmental variables in a fjord system influenced by both eutrophication and overfishing. A field survey was conducted over a coastal gradient comprising 300 data points sampled consistently for fish community and environmental data. Results from multivariate and univariate analyses supported each other, demonstrating that mesopredatory fish abundance at species and functional group level was positively related to the cover of structurally complex vegetation and negatively related to eutrophication, as measured by water transparency. Contrary to other studies showing an inverse relationship to piscivore abundance over time, the spatial distribution of mesopredatory fish was not locally regulated by the abundance of piscivorous fish, probably attributed to piscivores being at historically low levels due to previous overfishing. Mesopredatory fish abundance was highest in areas with high habitat quality and positively related to the abundance of piscivores, suggesting a predominance of bottom-up processes. We conclude that, in parallel with ongoing regulations of fishing pressure, measures to restore habitat function and food web productivity are important for the recovery of coastal fish communities in the area.

  14. An updated assessment of Symbiodinium spp. that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B.

    PubMed

    Rouzé, Héloïse; Lecellier, Gaël J; Saulnier, Denis; Planes, Serge; Gueguen, Yannick; Wirshing, Herman H; Berteaux-Lecellier, Véronique

    2017-01-01

    The adaptative bleaching hypothesis (ABH) states that, depending on the symbiotic flexibility of coral hosts (i.e., the ability of corals to "switch" or "shuffle" their algal symbionts), coral bleaching can lead to a change in the composition of their associated Symbiodinium community and, thus, contribute to the coral's overall survival. In order to determine the flexibility of corals, molecular tools are required to provide accurate species delineations and to detect low levels of coral-associated Symbiodinium . Here, we used highly sensitive quantitative (real-time) PCR (qPCR) technology to analyse five common coral species from Moorea (French Polynesia), previously screened using only traditional molecular methods, to assess the presence of low-abundance (background) Symbiodinium spp. Similar to other studies, each coral species exhibited a strong specificity to a particular clade, irrespective of the environment. In addition, however, each of the five species harboured at least one additional Symbiodinium clade, among clades A-D, at background levels. Unexpectedly, and for the first time in French Polynesia, clade B was detected as a coral symbiont. These results increase the number of known coral- Symbiodinium associations from corals found in French Polynesia, and likely indicate an underestimation of the ability of the corals in this region to associate with and/or "shuffle" different Symbiodinium clades. Altogether our data suggest that corals from French Polynesia may favor a trade-off between optimizing symbioses with a specific Symbiodinium clade(s), maintaining associations with particular background clades that may play a role in the ability of corals to respond to environmental change.

  15. Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades.

    PubMed

    Baker, David M; Andras, Jason P; Jordán-Garza, Adán Guillermo; Fogel, Marilyn L

    2013-06-01

    Many reef-building corals form symbioses with dinoflagellates from the diverse genus Symbiodinium. There is increasing evidence of functional significance to Symbiodinium diversity, which affects the coral holobiont's response to changing environmental conditions. For example, corals hosting Symbiodinium from the clade D taxon exhibit greater resistance to heat-induced coral bleaching than conspecifics hosting the more common clade C. Yet, the relatively low prevalence of clade D suggests that this trait is not advantageous in non-stressful environments. Thus, clade D may only be able to out-compete other Symbiodinium types within the host habitat when conditions are chronically stressful. Previous studies have observed enhanced photosynthesis and fitness by clade C holobionts at non-stressful temperatures, relative to clade D. Yet, carbon-centered metrics cannot account for enhanced growth rates and patterns of symbiont succession to other genetic types when nitrogen often limits reef productivity. To investigate the metabolic costs of hosting thermally tolerant symbionts, we examined the assimilation and translocation of inorganic (15)N and (13)C in the coral Acropora tenuis experimentally infected with either clade C (sub-type C1) or D Symbiodinium at 28 and 30 °C. We show that at 28 °C, C1 holobionts acquired 22% more (15)N than clade D. However, at 30 °C, C1 symbionts acquired equivalent nitrogen and 16% less carbon than D. We hypothesize that C1 competitively excludes clade D in hospite via enhanced nitrogen acquisition and thus dominates coral populations despite warming oceans.

  16. EMBATTLED BIVALVES: BIOGEOGRAPHIC DISTRIBUTIONS AND ABUNDANCES FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

    EPA Science Inventory

    As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change, we have synthesized in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT), the biogeographic distributions and abundances of bivalves, found in dept...

  17. Sand fly (Diptera: Psychodidae) abundance and species diversity in relation to environmental factors in parts of coastal plains of southern India.

    PubMed

    Srinivasan, R; Jambulingam, P; Vanamail, P

    2013-07-01

    Abundance pattern of sand flies in relation to several environmental factors, such as type of areas, dwellings, landforms, land usage pattern, and surface soil pH, was assessed in 81 areas or villages of Puducherry district, Puducherry Union Territory, located on the coastal plain of southern India, for three seasons, between November 2006 and October 2008, adopting hand-catch method. In total, 1,319 sand fly specimens comprising 12 species under two genera, viz., Phlebotomus and Sergentomyia, were collected. Among them, Phlebotomus (Euphlebotomus) argentipes Annandale & Brunetti, the vector of visceral leishmaniasis in India, was the predominant species in all habitats surveyed. The hierarchical cluster analysis showed that the density of sand flies was 10-fold higher in high-density group and fivefold higher in medium-density group, compared with the no or low-density group. Sand fly density was found to be influenced significantly with the type of areas, dwellings, landforms, land usage pattern, and surface soil pH in different groups. Rural areas located on fluvial landform with alkaline surface soil pH, supporting rice cultivation and luxuriant vegetation, are the most influencing factors that favor sand fly abundance and diversity in this district.

  18. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord.

    PubMed

    Vader, Anna; Laughinghouse, Haywood D; Griffiths, Colin; Jakobsen, Kjetill S; Gabrielsen, Tove M

    2018-02-01

    Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Why should we investigate the morphological disparity of plant clades?

    PubMed Central

    Oyston, Jack W.; Hughes, Martin; Gerber, Sylvain; Wills, Matthew A.

    2016-01-01

    Background Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological ‘design’ space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Methods Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Key Results Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Conclusions Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused

  20. Clade age and species richness are decoupled across the eukaryotic tree of life.

    PubMed

    Rabosky, Daniel L; Slater, Graham J; Alfaro, Michael E

    2012-08-01

    Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

  1. Progress to extinction: increased specialisation causes the demise of animal clades.

    PubMed

    Raia, P; Carotenuto, F; Mondanaro, A; Castiglione, S; Passaro, F; Saggese, F; Melchionna, M; Serio, C; Alessio, L; Silvestro, D; Fortelius, M

    2016-08-10

    Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

  2. Progress to extinction: increased specialisation causes the demise of animal clades

    NASA Astrophysics Data System (ADS)

    Raia, P.; Carotenuto, F.; Mondanaro, A.; Castiglione, S.; Passaro, F.; Saggese, F.; Melchionna, M.; Serio, C.; Alessio, L.; Silvestro, D.; Fortelius, M.

    2016-08-01

    Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

  3. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

    PubMed Central

    Durham, Bryndan P.; Grote, Jana; Whittaker, Kerry A.; Bender, Sara J.; Luo, Haiwei; Grim, Sharon L.; Brown, Julia M.; Casey, John R.; Dron, Antony; Florez-Leiva, Lennin; Krupke, Andreas; Luria, Catherine M.; Mine, Aric H.; Nigro, Olivia D.; Pather, Santhiska; Talarmin, Agathe; Wear, Emma K.; Weber, Thomas S.; Wilson, Jesse M.; Church, Matthew J.; DeLong, Edward F.; Karl, David M.; Steward, Grieg F.; Eppley, John M.; Kyrpides, Nikos C.; Schuster, Stephan; Rappé, Michael S.

    2014-01-01

    Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters. PMID:25197450

  4. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.

    PubMed

    Durham, Bryndan P; Grote, Jana; Whittaker, Kerry A; Bender, Sara J; Luo, Haiwei; Grim, Sharon L; Brown, Julia M; Casey, John R; Dron, Antony; Florez-Leiva, Lennin; Krupke, Andreas; Luria, Catherine M; Mine, Aric H; Nigro, Olivia D; Pather, Santhiska; Talarmin, Agathe; Wear, Emma K; Weber, Thomas S; Wilson, Jesse M; Church, Matthew J; DeLong, Edward F; Karl, David M; Steward, Grieg F; Eppley, John M; Kyrpides, Nikos C; Schuster, Stephan; Rappé, Michael S

    2014-06-15

    Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

  5. Rapid Differentiation between Livestock-Associated and Livestock-Independent Staphylococcus aureus CC398 Clades

    PubMed Central

    Larsen, Jesper; Soldanova, Katerina; Aziz, Maliha; Contente-Cuomo, Tania; Petersen, Andreas; Vandendriessche, Stien; Jiménez, Judy N.; Mammina, Caterina; van Belkum, Alex; Salmenlinna, Saara; Laurent, Frederic; Skov, Robert L.; Larsen, Anders R.; Andersen, Paal S.; Price, Lance B.

    2013-01-01

    Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet(M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clades and the duplex PCR assay correctly identified scn and tet(M). The assays were successfully applied to a geographically diverse collection of 272 human S. aureus CC398 isolates. The simple assays described here generate signals comparable to a whole-genome phylogeny for major clade assignment and are easily integrated into S. aureus CC398 surveillance programs and epidemiological studies. PMID:24244535

  6. The Longibrachiatum Clade of Trichoderma: a revision with new species

    USDA-ARS?s Scientific Manuscript database

    The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic ke...

  7. Rapid Identification of Different Escherichia coli Sequence Type 131 Clades.

    PubMed

    Matsumura, Yasufumi; Pitout, Johann D D; Peirano, Gisele; DeVinney, Rebekah; Noguchi, Taro; Yamamoto, Masaki; Gomi, Ryota; Matsuda, Tomonari; Nakano, Satoshi; Nagao, Miki; Tanaka, Michio; Ichiyama, Satoshi

    2017-08-01

    Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone resistance and extended-spectrum-β-lactamase (ESBL) producers. The members of ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C), as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in two Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli isolates from extraintestinal sites (ExPEC) (2014). The assay correctly identified the different clades in all 80 global isolates: clades A ( n = 12), B ( n = 12), and C, including subclades C1-M27 ( n = 16), C1-nM27 ( n = 20), C2 ( n = 17), and other C ( n = 3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A ( n = 54), B ( n = 23), and C ( n = 483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with bla CTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli isolates and is a promising tool for epidemiological studies of ST131. Copyright © 2017 American Society for Microbiology.

  8. Why should we investigate the morphological disparity of plant clades?

    PubMed

    Oyston, Jack W; Hughes, Martin; Gerber, Sylvain; Wills, Matthew A

    2016-04-01

    Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and

  9. High-resolution climate of the past ∼7300 years of coastal northernmost California: Results from diatoms, silicoflagellates, and pollen

    USGS Publications Warehouse

    Barron, John A.; Bukry, David; Heusser, Linda E.; Addison, Jason A.; Alexander, Clark R.

    2018-01-01

    Piston core TN062-O550, collected about 33 km offshore of Eureka, California, contains a high-resolution record of the climate and oceanography of coastal northernmost California during the past ∼7.34 kyr. Chronology established by nine AMS ages on a combination of planktic foraminifers, bivalve shell fragments, and wood yields a mean sedimentation rate of 103 cm kyr−1. Marine proxies (diatoms and silicoflagellates) and pollen transported by the nearby Eel River reveal a stepwise development of both modern offshore surface water oceanography and coastal arboreal ecosystems. Beginning at ∼5.4 cal ka the relative abundance of coastal redwood pollen, a proxy for coastal fog, displays a two fold increase suggesting enhanced coastal upwelling. A decline in the relative contribution of subtropical diatoms at ∼5.0 cal ka implies cooling of sea surface temperatures (SSTs). At ∼3.6 cal ka an increase in the relative abundance of alder and oak at the expense of coastal redwood likely signals intensified riverine transport of pollen from inland environments. Cooler offshore SSTs and increased precipitation characterize the interval between ∼3.6 and 2.8 cal ka. A rapid, stepwise change in coastal climatology and oceanography occurs between ∼2.8 and 2.6 cal ka that suggests an enhanced expression of modern Pacific Decadal Oscillation-like (PDO) cycles. A three-fold increase in the relative abundance of the subtropical diatom Fragilariopsis doliolus at 2.8 cal ka appears to mark an abrupt warming of winter SSTs. Soon afterwards at 2.6 cal ka, a two fold increase in the relative abundance of coastal redwood pollen is suggestive of an abrupt intensification of spring upwelling. After ∼2.8 cal ka a sequence of cool-warm, PDO-like cycles occurs wherein cool cycles are characterized by relative abundance increases in coastal redwood pollen and decreased contributions of subtropical diatoms, whereas opposite proxy trends distinguish warm cycles.

  10. Testing For Ecological Correlations between Greenhouse Gas Fluxes and their Potential Biotic Drivers in Coastal Wetlands

    EPA Science Inventory

    The role of coastal wetlands in ameliorating the plight of climate change is well documented. Per unit area, coastal wetlands are among the largest natural carbon sinks, taking up abundant carbon dioxide (CO2) and emitting minimal methane (CH4). While the role of coastal marsh ...

  11. Spatio-temporal niche partitioning of closely related picocyanobacteria clades and phycocyanin pigment types in Lake Constance (Germany).

    PubMed

    Becker, Sven; Sánchez-Baracaldo, Patricia; Singh, Arvind K; Hayes, Paul K

    2012-05-01

    We found that the clade-specific abundance dynamics of Synechococcus type picocyanobacteria in the pelagic and littoral zone macro-habitats of Lake Constance (Germany) challenge the hypothesis of a regular annual succession of picocyanobacteria genotypes in temperate zone lakes. Methods used in this study were quantitative Taq nuclease assays (TNA), denaturing gradient gel electrophoresis (DGGE), a 19-month time series analysis (with two isothermal and two stratified periods) and genotyping of a new littoral phycocyanin (PC)-rich Synechococcus strain collection. The recorded differences between the two macro-habitats and between seasons or years, and the observed effect of water column mixis in winter on the inversion of clade-specific dominance ratios in Lake Constance might explain the known inter-annual differences in abundance and dynamics of the autotrophic picoplankton (APP) in lakes. The APP in Lake Constance shows a high genetic diversity with a low overall abundance, similar to the APP in the Baltic Sea, but different from Lake Biwa in Japan or lakes in the UK. Our results indicate that APP bloom events in both macro-habitats of Lake Constance are driven by phycoerythrin-rich Synechococcus genotypes of the Subalpine Cluster I. DGGE revealed the presence of a diverse periphyton (biofilm) community of the PC-rich Synechococcus pigment type in the littoral zone in early spring, when no such community was detectable in the pelagic habitat. A more sensitive and quantitative approach with TNA, however, revealed an intermittent presence of one PC-rich genotype in the plankton. We discuss the seasonal development of the pelagic and littoral PC-rich community, and while we cannot rule out a strain isolation bias, we found that isolated PC-rich strains from the pelagic habitat have different genotypes when compared to new littoral strains. We also observed littoral substrates colonized by specific PC-rich Synechococcus genotypes. © 2012 Federation of European

  12. Stickleback increase in the Baltic Sea - A thorny issue for coastal predatory fish

    NASA Astrophysics Data System (ADS)

    Bergström, Ulf; Olsson, Jens; Casini, Michele; Eriksson, Britas Klemens; Fredriksson, Ronny; Wennhage, Håkan; Appelberg, Magnus

    2015-09-01

    In the Baltic Sea, the mesopredator three-spined stickleback (Gasterosteus aculeatus) spends a large part of its life cycle in the open sea, but reproduces in shallow coastal habitats. In coastal waters, it may occur in high abundances, is a potent predator on eggs and larvae of fish, and has been shown to induce trophic cascades with resulting eutrophication symptoms through regulation of invertebrate grazers. Despite its potential significance for the coastal food web, little is known about its life history and population ecology. This paper provides a description of life history traits, migration patterns and spatiotemporal development of the species in the Baltic Sea during the past decades, and tests the hypothesis that stickleback may have a negative impact on populations of coastal predatory fish. Offshore and coastal data during the last 30 years show that stickleback has increased fourfold in the Bothnian Sea, 45-fold in the Central Baltic Sea and sevenfold in the Southern Baltic Sea. The abundances are similar in the two northern basins, and two orders of magnitude lower in the Southern Baltic Sea. The coastward spawning migration of sticklebacks from offshore areas peaks in early May, with most spawners being two years of age at a mean length of 65 mm. The early juvenile stage is spent at the coast, whereafter sticklebacks perform a seaward feeding migration in early autumn at a size of around 35 mm. A negative spatial relation between the abundance of stickleback and early life stages of perch and pike at coastal spawning areas was observed in spatial survey data, indicating strong interactions between the species. A negative temporal relationship was observed also between adult perch and stickleback in coastal fish monitoring programmes supporting the hypothesis that stickleback may have negative population level effects on coastal fish predators. The recent increase in stickleback populations in different basins of the Baltic Sea in combination with

  13. Insights into the activity of maturation inhibitor PF-46396 on HIV-1 clade C.

    PubMed

    Ghimire, Dibya; Timilsina, Uddhav; Srivastava, Tryambak Pratap; Gaur, Ritu

    2017-03-02

    HIV maturation inhibitors are an emerging class of anti-retroviral compounds that inhibit the viral protease-mediated cleavage of the Gag, CA-SP1 (capsid-spacer peptide 1) peptide to mature CA. The first-in-class maturation inhibitor bevirimat (BVM) displayed potent activity against HIV-1 clade B but was ineffective against other HIV-1 clades including clade C. Another pyridone-based maturation inhibitor, PF-46396 displayed potent activity against HIV-1 clade B. In this study, we aimed at determining the activity of PF-46396 against HIV-1 clade C. We employed various biochemical and virological assays to demonstrate that PF-46396 is effective against HIV-1 clade C. We observed a dose dependent accumulation of CA-SP1 intermediate in presence of the compound. We carried out mutagenesis in the CA- SP1 region of HIV-1 clade C Gag and observed that the mutations conferred resistance against the compound. Many mutations inhibited Gag processing thereby reducing virus release in the absence of the compound. However, presence of PF-46396 rescued these defects and enhanced virus release, replication capacity and infectivity of HIV-1 clade C. These results put together identify PF-46396 as a broadly active maturation inhibitor against HIV-1 clade B and C and help in rational designing of novel analogs with reduced toxicity and increased efficacy for its potential use in clinics.

  14. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    PubMed Central

    Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki

    2016-01-01

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage. PMID:26613339

  15. [Effect of flooding time on community structure and abundance of Geobacteraceae in paddy soil].

    PubMed

    You, Jiaohua; Xia, Shuhong; Wang, Baoli; Qu, Dong

    2011-06-01

    The dynamic characteristics of community structure and relative abundance of Geobacteraceae were investigated to understand their response to microbial iron (III) reducing in flooded paddy soil. The paddy soil was incubated anaerobically and the amount of Fe(II) was determined during the flooding incubation. We retrieved Geobacteraceae sequences from clone libraries constructed for different time points (1 h and day 1, 5, 10, 20 and 30) after flooding of the paddy soil. The diversity and community structure were analyzed by using RFLP method, and the relative abundance of Geobacteraceae was detected by real-time PCR. Microbial reduction of iron (III) changed greatly in early time and was stable after incubated for 20 d in paddy soil. The largest iron reduction potential was 10.16 mg/g with a Vmax of 1.064 mg/(g x d) at the time of 4.84 d whereas this process achieved plateau after 20 days flooding. Diversity of Geobacteraceae, given by alpha indices, fluctuated during the flooding incubation. Two peaks of diversity were observed in treatments of 5 d and 20 d respectively, while significant low diversity appeared in samples of 10 d and 30 d. Beta indices described the differences between community structures of Geobacteraceae and hence reflected the variation of the flooding situation over time. In all samples, 10 RFLP-based preponderant types were found, which fell into clade 1 and clade 2 of Geobacteraceae. The relative abundance of Geobacteraceae was the lowest in 1 d (1.20% ) and the highest in 20 d (4.54%). The dynamic variation of Geobacteraceae diversity, community structure and abundance are closely related to microbial iron (III) reducing in flooding paddy soil.

  16. Development and validation of broad-range qualitative and clade-specific quantitative molecular probes for assessing mercury methylation in the environment

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Christensen, Geoff A.; Wymore, Ann M.; King, Andrew J.

    Two genes, hgcA and hgcB, are essential for microbial mercury (Hg)-methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability and biogeochemistry is critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea. A distinct PCR product at the expected size was confirmed for all hgcAB+ strains tested via Sanger sequencing.more » Additionally, we developed clade-specific degenerate quantitative primers (qPCR) that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88% and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. Here, the resulting data will be essential in developing accurate and robust predictive models of Hg-methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB.« less

  17. Development and validation of broad-range qualitative and clade-specific quantitative molecular probes for assessing mercury methylation in the environment

    DOE PAGES

    Christensen, Geoff A.; Wymore, Ann M.; King, Andrew J.; ...

    2016-07-15

    Two genes, hgcA and hgcB, are essential for microbial mercury (Hg)-methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability and biogeochemistry is critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea. A distinct PCR product at the expected size was confirmed for all hgcAB+ strains tested via Sanger sequencing.more » Additionally, we developed clade-specific degenerate quantitative primers (qPCR) that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88% and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. Here, the resulting data will be essential in developing accurate and robust predictive models of Hg-methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB.« less

  18. Potential retention effect at fish farms boosts zooplankton abundance

    NASA Astrophysics Data System (ADS)

    Fernandez-Jover, D.; Toledo-Guedes, K.; Valero-Rodríguez, J. M.; Fernandez-Gonzalez, V.; Sanchez-Jerez, P.

    2016-11-01

    Coastal aquaculture activities influence wild macrofauna in natural environments due to the introduction of artificial structures, such as floating cages, that provide structural complexity in the pelagic system. This alters the abundance and distribution of the affected species and also their feeding behaviour and diet. Despite this, the effects of coastal aquaculture on zooplankton assemblages and the potential changes in their abundance and distribution remain largely unstudied. Traditional plankton sampling hauls between the farm mooring systems entail some practical difficulties. As an alternative, light traps were deployed at 2 farms in the SW Mediterranean during a whole warm season. Total zooplankton capture by traps at farms was higher than at control locations on every sampling night. It ranged from 3 to 10 times higher for the taxonomic groups: bivalvia, cladocera, cumacea, fish early-life-stages, gastropoda, polychaeta and tanaidacea; 10-20 times higher for amphipoda, chaetognatha, isopoda, mysidacea and ostracoda, and 22 times higher for copepoda and the crustacean juvenile stages zoea and megalopa. Permutational analysis showed significant differences for the most abundant zooplankton groups (copepoda, crustacean larvae, chaetognatha, cladocera, mysidacea and polychaeta). This marked incremental increase in zooplankton taxa at farms was consistent, irrespective of the changing environmental variables registered every night. Reasons for the greater abundance of zooplankton at farms are discussed, although results suggest a retention effect caused by cage structures rather than active attraction through physical or chemical cues.

  19. Origin and Dispersal History of Two Colonial Ascidian Clades in the Botryllus schlosseri Species Complex.

    PubMed

    Nydam, Marie L; Giesbrecht, Kirsten B; Stephenson, Emily E

    2017-01-01

    Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species. Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin for Clade A, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species. Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin of Clade E on the French side of the English Channel. An unsampled lineage evolved from the French lineage, which reflects the conclusion from the median joining network that not all Clade E lineages have been sampled. This unsampled lineage gave rise to the haplotypes on the English side of the English Channel, which were the ancestors to the Mediterranean and Bay of Biscay populations. Clade E has a wider geographic range than previously thought, and shows evidence of recent range expansion. Both Clade A and Clade E should be considered widespread species: Clade A globally and Clade E within Europe.

  20. Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle

    PubMed Central

    Takano, Shun-ichiro; Tuda, Midori; Takasu, Keiji; Furuya, Naruto; Imamura, Yuya; Kim, Sangwan; Tashiro, Kosuke; Iiyama, Kazuhiro; Tavares, Matias; Amaral, Acacio Cardoso

    2017-01-01

    Maternally inherited bacterial endosymbionts in arthropods manipulate host reproduction to increase the fitness of infected females. Cytoplasmic incompatibility (CI) is one such manipulation, in which uninfected females produce few or no offspring when they mate with infected males. To date, two bacterial endosymbionts, Wolbachia and Cardinium, have been reported as CI inducers. Only Wolbachia induces complete CI, which causes 100% offspring mortality in incompatible crosses. Here we report a third CI inducer that belongs to a unique clade of Alphaproteobacteria detected within the coconut beetle, Brontispa longissima. This beetle comprises two cryptic species, the Asian clade and the Pacific clade, which show incompatibility in hybrid crosses. Different bacterial endosymbionts, a unique clade of Alphaproteobacteria in the Pacific clade and Wolbachia in the Asian clade, induced bidirectional CI between hosts. The former induced complete CI (100% mortality), whereas the latter induced partial CI (70% mortality). Illumina MiSeq sequencing and denaturing gradient gel electrophoresis patterns showed that the predominant bacterium detected in the Pacific clade of B. longissima was this unique clade of Alphaproteobacteria alone, indicating that this endosymbiont was responsible for the complete CI. Sex distortion did not occur in any of the tested crosses. The 1,160 bp of 16S rRNA gene sequence obtained for this endosymbiont had only 89.3% identity with that of Wolbachia, indicating that it can be recognized as a distinct species. We discuss the potential use of this bacterium as a biological control agent. PMID:28533374

  1. Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

    PubMed Central

    Nandi, Tannistha; Holden, Matthew T.G.; Didelot, Xavier; Mehershahi, Kurosh; Boddey, Justin A.; Beacham, Ifor; Peak, Ian; Harting, John; Baybayan, Primo; Guo, Yan; Wang, Susana; How, Lee Chee; Sim, Bernice; Essex-Lopresti, Angela; Sarkar-Tyson, Mitali; Nelson, Michelle; Smither, Sophie; Ong, Catherine; Aw, Lay Tin; Hoon, Chua Hui; Michell, Stephen; Studholme, David J.; Titball, Richard; Chen, Swaine L.; Parkhill, Julian

    2015-01-01

    Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity. PMID:25236617

  2. Coupling molecules and morphology to discover new clades of ciliates.

    NASA Astrophysics Data System (ADS)

    Grattepanche, J. D.; Maurer-Alcalá, X. X.; Tucker, S. J.; McManus, G. B.; Katz, L. A.

    2016-02-01

    In a previous study using high-throughput sequencing (Grattepanche et al submitted, oral presentation?), we observe the presence of two clades of spirotrich ciliates mainly present in marine deep-water along the New England coast. These clades, clusters X1 and X2, are characterized by several deletions in their SSU-rDNA and have been observed elsewhere as both identical and similar sequences have been deposited on GenBank from other environmental studies, but lack morphological description. In order to link molecules (SSU-rDNA sequence) to their morphology, we sample below the photic zone (between 60 to 400m of depth) in the New England coast (Northeast Atlantic) in a transect crossing the continental shelf. We designed an oligonucleotide probe specific for choreotrich and oligotrich ciliates and another specific to clusters X1 and X2 to describe these clades through a combination of Fluorescence In Situ Hybridization (FISH) and light microscopy. Our aim is to increase our knowledge on the morphology of these `unknown' clades of ciliates, which will allow for future ecological studies.

  3. Dynamics of clade diversification on the morphological hypercube

    PubMed Central

    Gavrilets, S.

    1999-01-01

    Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade's expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade's growth rate.

  4. Concentration-Dependent Patterns of Leucine Incorporation by Coastal Picoplankton

    PubMed Central

    Alonso, Cecilia; Pernthaler, Jakob

    2006-01-01

    Coastal pelagic environments are believed to feature concentration gradients of dissolved organic carbon at a microscale, and they are characterized by pronounced seasonal differences in substrate availability for the heterotrophic picoplankton. Microbial taxa that coexist in such habitats might thus differ in their ability to incorporate substrates at various concentrations. We investigated the incorporation patterns of leucine in four microbial lineages from the coastal North Sea at concentrations between 0.1 and 100 nM before and during a spring phytoplankton bloom. Community bulk incorporation rates and the fraction of leucine-incorporating cells in the different populations were analyzed. Significantly fewer bacterial cells incorporated the amino acid before (13 to 35%) than during (23 to 47%) the bloom at all but the highest concentration. The incorporation rate per active cell in the prebloom situation was constant above 0.1 nM added leucine, whereas it increased steeply with substrate concentration during the bloom. At both time points, a high proportion of members of the Roseobacter clade incorporated leucine at all concentrations (55 to 80% and 86 to 94%, respectively). In contrast, the fractions of leucine-incorporating cells increased substantially with substrate availability in bacteria from the SAR86 clade (8 to 31%) and from DE cluster 2 of the Flavobacteria-Sphingobacteria (14 to 33%). The incorporation patterns of marine Euryarchaeota were between these extremes (30 to 56% and 48 to 70%, respectively). Our results suggest that the contribution of microbial taxa to the turnover of particular substrates may be concentration dependent. This may help us to understand the specific niches of coexisting populations that appear to compete for the same resources. PMID:16517664

  5. Herbivory increases diversification across insect clades

    PubMed Central

    Wiens, John J.; Lapoint, Richard T.; Whiteman, Noah K.

    2015-01-01

    Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life. PMID:26399434

  6. Herbivory increases diversification across insect clades.

    PubMed

    Wiens, John J; Lapoint, Richard T; Whiteman, Noah K

    2015-09-24

    Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.

  7. Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

    PubMed Central

    Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

    2017-01-01

    Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

  8. Differential Distributions of Synechococcus Subgroups Across the California Current System

    PubMed Central

    Paerl, Ryan W.; Johnson, Kenneth S.; Welsh, Rory M.; Worden, Alexandra Z.; Chavez, Francisco P.; Zehr, Jonathan P.

    2011-01-01

    Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system. PMID:21833315

  9. Freshwater availability and coastal wetland foundation species: ecological transitions along a rainfall gradient

    USGS Publications Warehouse

    Osland, Michael J.; Enwright, Nicholas M.; Stagg, Camille L.

    2014-01-01

    Climate gradient-focused ecological research can provide a foundation for better understanding critical ecological transition points and nonlinear climate-ecological relationships, which is information that can be used to better understand, predict, and manage ecological responses to climate change. In this study, we examined the influence of freshwater availability upon the coverage of foundation plant species in coastal wetlands along a northwestern Gulf of Mexico rainfall gradient. Our research addresses the following three questions: (1) what are the region-scale relationships between measures of freshwater availability (e.g., rainfall, aridity, freshwater inflow, salinity) and the relative abundance of foundation plant species in tidal wetlands; (2) How vulnerable are foundation plant species in tidal wetlands to future changes in freshwater availability; and (3) What is the potential future relative abundance of tidal wetland foundation plant species under alternative climate change scenarios? We developed simple freshwater availability-based models to predict the relative abundance (i.e., coverage) of tidal wetland foundation plant species using climate data (1970-2000), estuarine freshwater inflow-focused data, and coastal wetland habitat data. Our results identify regional ecological thresholds and nonlinear relationships between measures of freshwater availability and the relative abundance of foundation plant species in tidal wetlands. In drier coastal zones, relatively small changes in rainfall could produce comparatively large landscape-scale changes in foundation plant species abundance which would affect some ecosystem good and services. Whereas a drier future would result in a decrease in the coverage of foundation plant species, a wetter future would result in an increase in foundation plant species coverage. In many ways, the freshwater-dependent coastal wetland ecological transitions we observed are analogous to those present in dryland

  10. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    PubMed Central

    Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

    2008-01-01

    Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

  11. Patterns of Seasonal Abundance and Social Segregation in Inland and Coastal Plain Swamp Sparrows in a Delaware Tidal Marsh

    EPA Science Inventory

    The Coastal Plain Swamp Sparrow (Melospiza georgiana nigrescens, CPSS) breeds in the coastal brackish marshes of the North American Mid-Atlantic States. During the non-breeding season, coastal brackish marshes are occupied by both this subspecies and two far more widespread inte...

  12. Phylogeny, evolutionary trends and classification of the Spathelia-Ptaeroxylon clade: morphological and molecular insights.

    PubMed

    Appelhans, M S; Smets, E; Razafimandimbison, S G; Haevermans, T; van Marle, E J; Couloux, A; Rabarison, H; Randrianarivelojosia, M; Kessler, P J A

    2011-06-01

    The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal

  13. Meteorological factors associated with abundance of airborne fungal spores over natural vegetation

    NASA Astrophysics Data System (ADS)

    Crandall, Sharifa G.; Gilbert, Gregory S.

    2017-08-01

    The abundance of airborne fungal spores in agricultural and urban settings increases with greater air temperature, relative humidity, or precipitation. The same meteorological factors that affect temporal patterns in spore abundance in managed environments also vary spatially across natural habitats in association with differences in vegetation structure. Here we investigated how temporal and spatial variation in aerial spore abundance is affected by abiotic (weather) and biotic (vegetation) factors as a foundation for predicting how fungi may respond to changes in weather and land-use patterns. We measured the phenology of airborne fungal spores across a mosaic of naturally occurring vegetation types at different time scales to describe (1) how spore abundance changes over time, (2) which local meteorological variables are good predictors for airborne spore density, and (3) whether spore abundance differs across vegetation types. Using an air volumetric vacuum sampler, we collected spore samples at 3-h intervals over a 120-h period in a mixed-evergreen forest and coastal prairie to measure diurnal, nocturnal, and total airborne spore abundance across vegetation types. Spore samples were also collected at weekly and monthly intervals in mixed-evergreen forest, redwood forest, and maritime chaparral vegetation types from 12 field sites across two years. We found greater airborne spore densities during the wetter winter months compared to the drier summer months. Mean total spore abundance in the mixed-evergreen forest was twice than in the coastal prairie, but there were no significant differences in total airborne spore abundance among mixed-evergreen forest, redwood forest, and maritime chaparral vegetation types. Weekly and monthly peaks in airborne spore abundance corresponded with rain events and peaks in soil moisture. Overall, temporal patterns in meteorological factors were much more important in determining airborne fungal spore abundance than the

  14. Need Analysis of Coastal Fisherman empowerment Based on Economics education and Potential Coastal in Minahasa Regency of North Sulawesi

    NASA Astrophysics Data System (ADS)

    Wantah, Edwin; Djatmika, Ery Tri; Witjaksono, Mit; Wahyono, Hari

    2018-05-01

    This research article aims to describe the need analysis process of coastal fisherman empowerment in North Minahasa Regency of North Sulawesi Province through internalization of economics education and technical training based on potential coastal.This research used descriptive qualitative research design by using survey, field observational interview and Focus Group Discussion (FGD) method. The research subjects were 40 coastal fishermen in North Minahasa Regency spread in two sub-districts, namely Wori Sub-district and Kema Sub-district in North Minahasa Regency, who have capture capacity of 10 gross ton sand below. The results of needs analysis were identified in observation, in-depth interview, and Focus Group Discussion (FGD), which was confirmed by the survey results indicating that 87.5% of the coastal fishermen need knowledge and understanding of characteristics, attitudes and principles to become successful entrepreneurs, which can be implemented in productive business activities on coastal area, while 92.5% of the coastal fishermen require an understanding of creativity and innovation and its implementation, 90% of the coastal fishermen require knowledge of business diversification based on coastal area and marine potentials, 90% of the fishermen stated that they need knowledge and understanding of the process of processed fish products because of the abundant raw materials, 80% of the coastal fishermen said that they need an understanding of the way to establish business partnerships and business networks with other business groups, 90% of the coastal fishermen stated that they need an understanding of the way to form fishermen joint business groups and the way to develop the business group. 92.5% of the coastal fishermen need an understanding of business capital and the way to access business capital, and 85% of the coastal fishermen said that they need to understand money management, the way to plan proper financial allocations, and saving procedures

  15. Identification of potent maturation inhibitors against HIV-1 clade C.

    PubMed

    Timilsina, Uddhav; Ghimire, Dibya; Timalsina, Bivek; Nitz, Theodore J; Wild, Carl T; Freed, Eric O; Gaur, Ritu

    2016-06-06

    Antiretroviral therapy has led to a profound improvement in the clinical care of HIV-infected patients. However, drug tolerability and the evolution of drug resistance have limited treatment options for many patients. Maturation inhibitors are a new class of antiretroviral agents for treatment of HIV-1. They act by interfering with the maturation of the virus by blocking the last step in Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA by the viral protease (PR). The first-in-class maturation inhibitor bevirimat (BVM) failed against a subset of HIV-1 isolates in clinical trials due to polymorphisms present in the CA-SP1 region of the Gag protein. Sequence analysis indicated that these polymorphisms are more common in non-clade B strains of HIV-1 such as HIV-1 clade C. Indeed, BVM was found to be ineffective against HIV-1 clade C molecular clones tested in this study. A number of BVM analogs were synthesized by chemical modifications at the C-28 position to improve its activity. The new BVM analogs displayed potent activity against HIV-1 clade B and C and also reduced infectivity of the virus. This study identifies novel and broadly active BVM analogs that may ultimately demonstrate efficacy in the clinic.

  16. Anaerobic Ammonium Oxidation and its Contribution to Nitrogen Removal in China's Coastal Wetlands

    NASA Astrophysics Data System (ADS)

    Hou, L., Sr.

    2016-02-01

    Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China's coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China's coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8-10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China's coastal wetland ecosystems.

  17. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient

    PubMed Central

    Fortunato, Caroline S.; Crump, Byron C.

    2015-01-01

    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance

  18. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

    PubMed

    Fortunato, Caroline S; Crump, Byron C

    2015-01-01

    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance

  19. Patterns of rare and abundant marine microbial eukaryotes.

    PubMed

    Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angélique; Kooistra, Wiebe H C F; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sébastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A; de Vargas, Colomban; Massana, Ramon

    2014-04-14

    Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Comparing the Effects of Symbiotic Algae (Symbiodinium) Clades C1 and D on Early Growth Stages of Acropora tenuis

    PubMed Central

    Yuyama, Ikuko; Higuchi, Tomihiko

    2014-01-01

    Reef-building corals switch endosymbiotic algae of the genus Symbiodinium during their early growth stages and during bleaching events. Clade C Symbiodinium algae are dominant in corals, although other clades — including A and D — have also been commonly detected in juvenile Acroporid corals. Previous studies have been reported that only molecular data of Symbiodinium clade were identified within field corals. In this study, we inoculated aposymbiotic juvenile polyps with cultures of clades C1 and D Symbiodinium algae, and investigated the different effect of these two clades of Symbiodinium on juvenile polyps. Our results showed that clade C1 algae did not grow, while clade D algae grew rapidly during the first 2 months after inoculation. Polyps associated with clade C1 algae exhibited bright green fluorescence across the body and tentacles after inoculation. The growth rate of polyp skeletons was lower in polyps associated with clade C1 algae than those associated with clade D algae. On the other hand, antioxidant activity (catalase) of corals was not significantly different between corals with clade C1 and clade D algae. Our results suggested that clade D Symbiodinium algae easily form symbiotic relationships with corals and that these algae could contribute to coral growth in early symbiosis stages. PMID:24914677

  1. Phylogeny, evolutionary trends and classification of the Spathelia–Ptaeroxylon clade: morphological and molecular insights

    PubMed Central

    Appelhans, M. S.; Smets, E.; Razafimandimbison, S. G.; Haevermans, T.; van Marle, E. J.; Couloux, A.; Rabarison, H.; Randrianarivelojosia, M.; Keßler, P. J. A.

    2011-01-01

    Background and Aims The Spathelia–Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia–Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia–Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL–trnF, rps16 and psbA–trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila–Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia–Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities

  2. Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4).

    PubMed

    Shiratori, Takashi; Ishida, Ken-Ichiro

    2016-11-01

    A novel cercozoan filose thecate amoeba, Trachyrhizium urniformis n. g., n. sp., was isolated from a marine sediment sample collected at Agenashiku Island, Okinawa, Japan. We performed light and electron microscopic observations, and a molecular phylogenetic analysis using the small subunit ribosomal RNA gene of the isolate. Cells of T. urniformis are spherical in shape and are covered by a thin theca possessing a wide rounded aperture. Branching and occasionally anastomosing filopodia with small granules emerge from the aperture. The granules are transported in the filopodia bidirectionally. Transmission electron microscopy showed that cells of T. urniformis possess nucleus with permanently condensed chromatin, Golgi apparatuses, microbodies, mitochondria with tubular cristae, and extrusomes. Several morphological and ultrastructural features of T. urniformis (the presence of thecae and nucleus with permanently condensed chromatin) show similarities with those of Thecofilosea. In a phylogenetic analysis, T. urniformis included in Thecofilosea with weak statistical supports and formed a clade with two sequences that constitutes a cercozoan environmental clade, novel clade 4. On the basis of morphological and ultrastructural information and the results of the phylogenetic analysis, we propose T. urniformis as a new member of class Thecofilosea. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  3. Diatoms Si uptake capacity drives carbon export in coastal upwelling systems

    NASA Astrophysics Data System (ADS)

    Abrantes, Fatima; Cermeno, Pedro; Lopes, Cristina; Romero, Oscar; Matos, Lélia; Van Iperen, Jolanda; Rufino, Marta; Magalhães, Vitor

    2016-07-01

    Coastal upwelling systems account for approximately half of global ocean primary production and contribute disproportionately to biologically driven carbon sequestration. Diatoms, silica-precipitating microalgae, constitute the dominant phytoplankton in these productive regions, and their abundance and assemblage composition in the sedimentary record is considered one of the best proxies for primary production. The study of the sedimentary diatom abundance (SDA) and total organic carbon content (TOC) in the five most important coastal upwelling systems of the modern ocean (Iberia-Canary, Benguela, Peru-Humboldt, California, and Somalia-Oman) reveals a global-scale positive relationship between diatom production and organic carbon burial. The analysis of SDA in conjunction with environmental variables of coastal upwelling systems such as upwelling strength, satellite-derived net primary production, and surface water nutrient concentrations shows different relations between SDA and primary production on the regional scale. On the global scale, SDA appears modulated by the capacity of diatoms to take up silicic acid, which ultimately sets an upper limit to global export production in these ocean regions.

  4. The Temporal Dynamics of Coastal Phytoplankton and Bacterioplankton in the Eastern Mediterranean Sea

    PubMed Central

    Raveh, Ofrat; David, Niv; Rilov, Gil; Rahav, Eyal

    2015-01-01

    This study considers variability in phytoplankton and heterotrophic bacterial abundances and production rates, in one of the most oligotrophic marine regions in the world–the Levantine Basin. The temporal dynamics of these planktonic groups were studied in the coastal waters of the southeastern Mediterranean Sea approximately every two weeks for a total of two years. Heterotrophic bacteria were abundant mostly during late summer and midwinter, and were positively correlated with bacterial production and with N2 fixation. Based on size fractionating, picophytoplankton was abundant during the summer, whereas nano-microphytoplankton predominated during the winter and early spring, which were also evident in the size-fractionated primary production rates. Autotrophic abundance and production correlated negatively with temperature, but did not correlate with inorganic nutrients. Furthermore, a comparison of our results with results from the open Levantine Basin demonstrates that autotrophic and heterotrophic production, as well as N2 fixation rates, are considerably higher in the coastal habitat than in the open sea, while nutrient levels or cell abundance are not different. These findings have important ecological implications for food web dynamics and for biological carbon sequestration in this understudied region. PMID:26474399

  5. Evolution of pollination niches in a generalist plant clade.

    PubMed

    Gómez, José María; Perfectti, Francisco; Abdelaziz, Mohamed; Lorite, Juan; Muñoz-Pajares, Antonio Jesús; Valverde, Javier

    2015-01-01

    It is widely assumed that floral diversification occurs by adaptive shifts between pollination niches. In contrast to specialized flowers, identifying pollination niches of generalist flowers is a challenge. Consequently, how generalist pollination niches evolve is largely unknown. We apply tools from network theory and comparative methods to investigate the evolution of pollination niches among generalist species belonging to the genus Erysimum. These species have similar flowers. We found that the studied species may be grouped in several multidimensional niches separated not by a shift of pollinators, but instead by quantitative variation in the relative abundance of pollinator functional groups. These pollination niches did not vary in generalization degree; we did not find any evolutionary trend toward specialization within the studied clade. Furthermore, the evolution of pollination niche fitted to a Brownian motion model without phylogenetic signal, and was characterized by frequent events of niche convergences and divergences. We presume that the evolution of Erysimum pollination niches has occurred mostly by recurrent shifts between slightly different generalized pollinator assemblages varying spatially as a mosaic and without any change in specialization degree. Most changes in pollination niches do not prompt floral divergence, a reason why adaptation to pollinators is uncommon in generalist plants. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  6. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

    PubMed Central

    Malmstrom, Rex R; Rodrigue, Sébastien; Huang, Katherine H; Kelly, Libusha; Kern, Suzanne E; Thompson, Anne; Roggensack, Sara; Berube, Paul M; Henn, Matthew R; Chisholm, Sallie W

    2013-01-01

    Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome—that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome. PMID:22895163

  7. Phytoplankton community composition in nearshore coastal waters of Louisiana

    EPA Science Inventory

    Phytoplankton community compositions within near-shore coastal and estuarine waters of Louisiana were characterized by relative abundance, biovolume, and taxonomic identification to genus and species when possible. The range of total nitrogen was 0.5 to 1.3 mg L-1 and total phos...

  8. Cetacean distribution and abundance in relation to oceanographic domains on the eastern Bering Sea shelf: 1999-2004

    NASA Astrophysics Data System (ADS)

    Friday, Nancy A.; Waite, Janice M.; Zerbini, Alexandre N.; Moore, Sue E.

    2012-06-01

    Visual line transect surveys for cetaceans were conducted on the eastern Bering Sea shelf in association with pollock stock assessment surveys aboard the NOAA ship Miller Freeman in June and July of 1999, 2000, 2002, and 2004. Transect survey effort ranged from 1188 km in 1999 to 3761 km in 2002. Fin whales (Balaenoptera physalus) were the most common large whale in all years except 2004 when humpback whales (Megaptera novaeangliae) were more abundant. Dall's porpoise (Phocoenoides dalli) were the most common small cetacean in all years. Abundance estimates were calculated by year for each oceanographic domain: coastal, middle, and outer/slope. The middle and outer/slope domains were divided into two strata ("north" and "south") because of variable survey effort. The distribution and abundance of baleen whales changed between the earlier (colder) and later (warmer) survey years. Fin whales consistently occupied the outer shelf and secondarily the middle shelf, and their abundance was an order of magnitude greater in cold compared to warm years. Humpback whales "lived on the margin" of the northern Alaska Peninsula, eastern Aleutian Islands and Bristol Bay; their preferred habitat is possibly associated with areas of high prey availability due to nutrient upwelling and aggregation mechanisms. Minke whales (Balaenoptera acutorostrata) occur shoreward of fin whales in the outer and middle shelf and in coastal habitats along the Alaska Peninsula. The highest abundance for this species was observed in a cold (1999) year. No clear relationship emerged for odontocetes with regard to warm and cold years. Dall's porpoise occupied both outer and middle domains and harbor porpoise (Phocoena phocoena) were more common in middle and coastal domains. This study provided a unique, broad-scale assessment of cetacean distribution and abundance on the eastern Bering Sea shelf and a baseline for future comparisons.

  9. Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

    PubMed

    Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

    2012-10-01

    Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  10. Anaerobic ammonium oxidation and its contribution to nitrogen removal in China’s coastal wetlands

    NASA Astrophysics Data System (ADS)

    Hou, Lijun; Zheng, Yanling; Liu, Min; Li, Xiaofei; Lin, Xianbiao; Yin, Guoyu; Gao, Juan; Deng, Fengyu; Chen, Fei; Jiang, Xiaofen

    2015-10-01

    Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China’s coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China’s coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8-10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China’s coastal wetland ecosystems.

  11. Anaerobic ammonium oxidation and its contribution to nitrogen removal in China’s coastal wetlands

    PubMed Central

    Hou, Lijun; Zheng, Yanling; Liu, Min; Li, Xiaofei; Lin, Xianbiao; Yin, Guoyu; Gao, Juan; Deng, Fengyu; Chen, Fei; Jiang, Xiaofen

    2015-01-01

    Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China’s coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China’s coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8–10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China’s coastal wetland ecosystems. PMID:26494435

  12. A functional genomic analysis of Arabidopsis thaliana PP2C clade D

    USDA-ARS?s Scientific Manuscript database

    In the reference dicot plant Arabidopsis thaliana, the PP2C family of P-protein phosphatases includes the products of 80 genes that have been separated into 10 multi-protein clades plus six singletons. Clade D includes the products of nine genes distributed among 3 chromosomes (PPD1, At3g12620; PPD2...

  13. The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

    PubMed Central

    Larget, Bret

    2013-01-01

    In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample. [Bayesian phylogenetics; conditional clade distributions; improved accuracy; posterior probabilities of trees.] PMID:23479066

  14. Arthropod abundance and seasonal bird use of bottomland forest harvest gaps

    Treesearch

    Christopher E. Moorman; Liessa T. Woen; John C. Kilgo; James L. Hanula; Scott Horn; Michael D. Ulyshen

    2012-01-01

    We investigated the influence of arthropod abundance and vegetation structure on shifts in avian use of canopy gap, gap edge, and surrounding forest understory in a bottomland hardwood forest in the Upper Coastal Plain of South Carolina. We compared captures of foliage-gleaning birds among locations during four periods (spring migration, breeding, post-breeding, and...

  15. Life cycle strategies of copepods in coastal upwelling zones

    NASA Astrophysics Data System (ADS)

    Peterson, W.

    1998-06-01

    Life cycles of copepods of coastal upwelling zones are of the multigenerational type—as many as 10 or more generations may be produced each year, depending upon water temperature, food concentration and length of the upwelling season. Abundant food resources and moderate temperature convey advantages to those copepods living in coastal upwelling zones, however, there is a clear disadvantage in that coastal upwelling zones are highly advective environments. Typically, water circulation patterns are such that surface waters are carried offshore, deeper waters carried onshore and most of the water column over the continental shelf is moving equatorward. The challenge to copepod species that inhabit upwelling systems is life cycle closure—how do eggs, nauplii, juveniles and adults avoid being swept out of these ecosystems in the face of persistent transport out of the system? In this review, I first list the species which dominate coastal upwelling ecosystems then discuss three variations on the multigenerational life cycle scheme that are observed in upwelling systems. The latter part of the review is devoted to discussion of how individuals are retained in the productive continental shelf waters within coastal upwelling ecosystems. The suggestion is made that the only copepod species that successfully achieve life cycle closure in such systems are those that are preadapted to upwelling circulation patterns. Our quantitative understanding of the relative importance of physical factors (such as advection) and biological factors (birth, growth, and mortality) on life cycle strategies and population dynamics is quite rudimentary. It would help our understanding if there were more field studies and more computer modeling studies that focused on seasonal cycles of abundance, development times and vertical distribution of life cycle stages, and measurements of water circulation patterns.

  16. Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks.

    PubMed

    Prinzing, Andreas; Ozinga, Wim A; Brändle, Martin; Courty, Pierre-Emmanuel; Hennion, Françoise; Labandeira, Conrad; Parisod, Christian; Pihain, Mickael; Bartish, Igor V

    2017-01-01

    Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  17. Pico and nanoplankton abundance and carbon stocks along the Brazilian Bight

    PubMed Central

    Lopes dos Santos, Adriana; Marie, Dominique; Helena Pellizari, Vivian; Pereira Brandini, Frederico; Vaulot, Daniel

    2016-01-01

    Pico and nanoplankton communities from the Southwest Atlantic Ocean along the Brazilian Bight are poorly described. The hydrography in this region is dominated by a complex system of layered water masses, which includes the warm and oligotrophic Tropical Water (TW), the cold and nutrient rich South Atlantic Central Water (SACW) and the Coastal Water (CW), which have highly variable properties. In order to assess how pico- and nanoplankton communities are distributed in these different water masses, we determined by flow cytometry the abundance of heterotrophic bacteria, Prochlorococcus, Synechococcus and autotrophic pico and nanoeukaryotes along three transects, extending from 23°S to 31°S and 39°W to 49°W. Heterotrophic bacteria (including archaea, maximum of 1.5 × 106 cells mL−1) were most abundant in Coastal and Tropical Water whereas Prochlorococcus was most abundant in open-ocean oligotrophic waters (maximum of 300 × 103 cells mL−1). Synechococcus(up to 81 × 103 cells mL−1), as well as autotrophic pico and nanoeukaryotes seemed to benefit from the influx of nutrient-rich waters near the continental slope. Autotrophic pico and nanoeukaryotes were also abundant in deep chlorophyll maximum (DCM) layers from offshore waters, and their highest abundances were 20 × 103 cells mL−1 and 5 × 103 cells mL−1, respectively. These data are consistent with previous observations in other marine areas where Synechococcus and autotrophic eukaryotes dominate mesotrophic waters, whereas Prochlorococcus dominate in more oligotrophic areas. Regardless of the microbial community structure near the surface, the carbon stock dominance by autotrophic picoeukaryotes near the DCM is possibly linked to vertical mixing of oligotrophic surface waters with the nutrient-rich SACW and their tolerance to lower light levels. PMID:27867760

  18. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.

    PubMed

    Stingl, Ulrich; Tripp, Harry James; Giovannoni, Stephen J

    2007-08-01

    The introduction of high-throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural sea water as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments, bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the internal transcribed spacer (ITS) region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represented a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino-acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.

  19. Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C

    PubMed Central

    Klasse, P. J.; Ozorowski, Gabriel; Cupo, Albert; Pugach, Pavel; Ringe, Rajesh P.; Golabek, Michael; van Gils, Marit J.; Guttman, Miklos; Lee, Kelly K.; Wilson, Ian A.; Butera, Salvatore T.; Ward, Andrew B.; Montefiori, David C.; Sanders, Rogier W.; Moore, John P.

    2016-01-01

    We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses. PMID:27627672

  20. The epipelagic fish community of Beaufort Sea coastal waters, Alaska

    USGS Publications Warehouse

    Jarvela, L.E.; Thorsteinson, L.K.

    1999-01-01

    A three-year study of epipelagic fishes inhabiting Beaufort Sea coastal waters in Alaska documented spatial and temporal patterns in fish distribution and abundance and examined their relationships to thermohaline features during summer. Significant interannual, seasonal, and geographical differences in surface water temperatures and salinities were observed. In 1990, sea ice was absent and marine conditions prevailed, whereas in 1988 and 1991, heavy pack ice was present and the dissolution of the brackish water mass along the coast proceeded more slowly. Arctic cod, capelin, and liparids were the most abundant marine fishes in the catches, while arctic cisco was the only abundant diadromous freshwater species. Age-0 arctic cod were exceptionally abundant and large in 1990, while age-0 capelin dominated in the other years. The alternating numerical dominances of arctic cod and age-0 capelin may represent differing species' responses to wind-driven oceanographic processes affecting growth and survival. The only captures of age-0 arctic cisco occurred during 1990. Catch patterns indicate they use a broad coastal migratory corridor and tolerate high salinities. As in the oceanographic data, geographical anti temporal patterns were apparent in the fish catch data, but in most cases these patterns were not statistically testable because of excessive zero catches. The negative binomial distribution appeared to be a suitable statistical descriptor of the aggregated catch patterns for the more common species.

  1. Rapid sewage pollution assessment by means of the coverage of epilithic taxa in a coastal area in the SW Atlantic.

    PubMed

    Becherucci, M E; Jaubet, M L; Saracho Bottero, M A; Llanos, E N; Elías, R; Garaffo, G V

    2018-07-01

    The sewage pollution impact over coastal environment represents one of the main reasons explaining the deterioration of marine coastal ecosystems around the globe. This paper aims to detect promptly a putative sewage pollution impact in a Southwestern Atlantic coastal area of Argentina as well as to identify a straightforward way for monitoring, based on the relative abundance coverage of the intertidal epilithic taxa. Four sampling sites were distributed at increased distances from the sewage outfall where the cover of individual epilithic species was visually estimated. The surrounded outfall area (i.e. outfall site) resulted polluted with high percentages of organic matter in sediment and Enterococcus concentration in seawater. The structure of the community showed a remarkable difference between the polluted site (outfall site) and the unpolluted sites. The polychaete Boccardia proboscidea dominated the outfall site with variable abundances of the green algae Ulva sp. during the period of study, decreasing the diversity of the community, while the mussel Brachidontes rodriguezii and variable abundances of several algae species dominated the unpolluted sites. The monitoring of the benthic community represents an effective, non-destructive, relative inexpensive and rapid method to assess the health of the coastal environment in the study area. The large abundance of B. proboscidea along with the absence of B. rodriguezii individuals at <300m to the sewage outfall discharge allowed the success of this classical monitoring method in a temperate marine-coastal ecosystem with certain gradient of pollution. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Impacts of macro - and microplastic on macrozoobenthos abundance in intertidal zone

    NASA Astrophysics Data System (ADS)

    Bangun, A. P.; Wahyuningsih, H.; Muhtadi, A.

    2018-02-01

    Plastics pollution in coastal areas is one of the topics that have received more attention over the past few years. The intertidal zone is a waters area that is directly affected by contamination of plastic waste from land and sea. The purpose of this study was to analyze the types and abundance of plastic waste in the intertidal zone and its impact on macrozoobenthos abundance. This research was conducted at Pesisir Desa Jaring Halus in February-April 2017. Macrozoobenthos and macro - micro plastic were collected by using quadratic transect. Sediments were collected with a core, to a depth of 30 cm. Microplastic and macroplastic abundances were analyzed using separation of sediment density and hand sorting. The dominant micro plastic types were film (52.30%), fiber (24.88%), fragments (22.74%), followed by pellets (0.1%). The total number of microplastics were 326,33 items and macro plastic were 308 items. Macroplastic abundance is positively correlated with microplastic (0.765). The abundance of macrozoobenthos is negatively correlated with microplastic abundance (-0.368) and with macro plastic abundance (-0.633). The management strategies were suggested clean up marine debris, decrease plastic using and built up the station of debris processing.

  3. Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

    PubMed Central

    Bennett, Kristin P.

    2014-01-01

    We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

  4. High abundance of salps in the coastal Gulf of Alaska during 2011: A first record of bloom occurrence for the northern Gulf

    NASA Astrophysics Data System (ADS)

    Li, Kaizhi; Doubleday, Ayla J.; Galbraith, Moira D.; Hopcroft, Russell R.

    2016-10-01

    Atypical high abundances of two salp species occurred in the coastal Gulf of Alaska during 2011. Salpa aspera dominated numerically in aggregate form during spring, and became uncommon during summer, while Cyclosalpa bakeri increased from low during spring to high abundance during summer. Both species were absent, or nearly so, by fall. C. bakeri abundance was positively correlated to surface temperature in spring and summer, and both species abundances were negatively correlated to chlorophyll a. The proportion of aggregate forms of both species was higher than that of solitary forms during spring and summer. The length-frequency of S. aspera aggregate individuals ranged primarily from 10 to 50 mm, and solitary forms reached 130 mm, while C. bakeri aggregates were 10-25 mm, with solitary forms up to 75 mm. Estimated biomass of S. aspera was 0.35±0.64 mg C m-3 in southeastern Alaska during spring then decreased to 0.03±0.12 mg C m-3 during summer. Estimated biomass of C. bakeri was 0.03±0.06 mg C m-3 over the entire sampling domain during spring, then rose to 0.15±0.25 mg C m-3 during summer. The volume of water filtered daily by S. aspera was estimated to be up to 17% of the 200 m water column at some stations during spring, but only up to 3.5% during summer. Substantially higher grazing impact was possible if animals were largely confined to the surface mixed layer (typically 20-30 m thick). The average volume filtrated was higher during spring for S. aspera, but for C. bakeri it was higher during summer. We propose that the combined effect of the northward transport of seed populations, their rapid biomass increase through asexual reproduction, and the high clearance rate of salps contributed to atypically low chlorophyll a in the Gulf of Alaska during spring and summer of 2011. This unusual event impacted ecosystem function during 2011, and might be expected to increase in frequency as the Gulf continues to respond to climate variations.

  5. Phytoplankton community and environmental correlates in a coastal upwelling zone along western Taiwan Strait

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Kang, Jian-hua; Ye, You-yin; Lin, Geng-ming; Yang, Qing-liang; Lin, Mao

    2016-02-01

    Upwelling system in western Taiwan Strait is important for facilitating the fishery production. This study investigated hydro-chemical properties, phytoplankton biomass, phytoplankton species composition, three-dimensional (horizontal, vertical and transect) distribution of phytoplankton abundance, as well as phytoplankton annual variation and the correlation of phytoplankton community with the upwelling of underlying current and nutrients according to samples of Fujian-Guangdong coastal upwelling zone in western Taiwan Strait from August 27 to September 8, 2009. The results manifest that the nutrient-rich cold and high salinity current on the continental shelf of South China Sea upwells to the Fujian-Guangdong coastal waters through Taiwan Bank and the surging strength to surface is weak while strong at 30-m layer. The thermohaline center of coastal upwelling shifts to the east of Dongshan Island and expanded to offshore waters in comparison with previous records. A total of 137 phytoplankton species belonging to 59 genera in 4 phyla are identified excluding the unidentified species. Diatom is the first major group and followed by dinoflagellate. Cyanobacteria mainly composed by three Trichodesmium species account for a certain proportions, while Chrysophyta are only found in offshore waters. The dominant species include Thalassionema nitzschioides, Pseudo-nitzschia pungens, Thalassionema frauenfeldii, Pseudo-nitzschia delicatissima, Rhizosolenia styliformis, Chaetoceros curvisetus, Diplopsalis lenticula and Trichodesmium thiebautii. Phytoplankton community mainly consists of eurythermal and eurytopic species, followed by warm-water species, tropic high-salinity species and oceanic eurythermic species in order. Phytoplankton abundance ranges from 1.00 × 102 ind./L ~ 437.22 × 102 ind./L with an average of 47.36 × 102 ind./L. For vertical distribution, maximum abundance is found at 30 m-depth and the surface comes second. Besides, the abundance below 30 m

  6. When Can Clades Be Potentially Resolved with Morphology?

    PubMed Central

    Bapst, David W.

    2013-01-01

    Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of ‘intrinsic’ resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups. PMID:23638034

  7. Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

    PubMed

    Kurtzman, Cletus P; Robnett, Christie J; Blackwell, Meredith

    2016-08-01

    DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA. Published by Oxford University Press on behalf of FEMS 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  8. Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

    PubMed Central

    Tabuce, Rodolphe; Marivaux, Laurent; Adaci, Mohammed; Bensalah, Mustapha; Hartenberger, Jean-Louis; Mahboubi, Mohammed; Mebrouk, Fateh; Tafforeau, Paul; Jaeger, Jean-Jacques

    2007-01-01

    The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105–25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican ‘hyopsodontid condylarths’ (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals. PMID:17329227

  9. Coastal Upwelling Drives Intertidal Assemblage Structure and Trophic Ecology.

    PubMed

    Reddin, Carl J; Docmac, Felipe; O'Connor, Nessa E; Bothwell, John H; Harrod, Chris

    2015-01-01

    Similar environmental driving forces can produce similarity among geographically distant ecosystems. Coastal oceanic upwelling, for example, has been associated with elevated biomass and abundance patterns of certain functional groups, e.g., corticated macroalgae. In the upwelling system of Northern Chile, we examined measures of intertidal macrobenthic composition, structure and trophic ecology across eighteen shores varying in their proximity to two coastal upwelling centres, in a hierarchical sampling design (spatial scales of >1 and >10 km). The influence of coastal upwelling on intertidal communities was confirmed by the stable isotope values (δ13C and δ15N) of consumers, including a dominant suspension feeder, grazers, and their putative resources of POM, epilithic biofilm, and macroalgae. We highlight the utility of muscle δ15N from the suspension feeding mussel, Perumytilus purpuratus, as a proxy for upwelling, supported by satellite data and previous studies. Where possible, we used corrections for broader-scale trends, spatial autocorrelation, ontogenetic dietary shifts and spatial baseline isotopic variation prior to analysis. Our results showed macroalgal assemblage composition, and benthic consumer assemblage structure, varied significantly with the intertidal influence of coastal upwelling, especially contrasting bays and coastal headlands. Coastal topography also separated differences in consumer resource use. This suggested that coastal upwelling, itself driven by coastline topography, influences intertidal communities by advecting nearshore phytoplankton populations offshore and cooling coastal water temperatures. We recommend the isotopic values of benthic organisms, specifically long-lived suspension feeders, as in situ alternatives to offshore measurements of upwelling influence.

  10. Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.

    PubMed

    Tanaka, Mami; Endo, Shoko; Kotake, Fumihito; Al-Saari, Nurhidayu; Amin, A K M Rohul; Feng, Gao; Mino, Sayaka; Doi, Hidetaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Suda, Wataru; Hattori, Masahira; Yumoto, Isao; Sawabe, Toko; Sawabe, Tomoo; Araki, Toshiyoshi

    2017-01-01

    A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

  11. High-model abundance may permit the gradual evolution of Batesian mimicry: an experimental test

    PubMed Central

    Kikuchi, David W.; Pfennig, David W.

    2010-01-01

    In Batesian mimicry, a harmless species (the ‘mimic’) resembles a dangerous species (the ‘model’) and is thus protected from predators. It is often assumed that the mimetic phenotype evolves from a cryptic phenotype, but it is unclear how a population can transition through intermediate phenotypes; such intermediates may receive neither the benefits of crypsis nor mimicry. Here, we ask if selection against intermediates weakens with increasing model abundance. We also ask if mimicry has evolved from cryptic phenotypes in a mimetic clade. We first present an ancestral character-state reconstruction showing that mimicry of a coral snake (Micrurus fulvius) by the scarlet kingsnake (Lampropeltis elapsoides) evolved from a cryptic phenotype. We then evaluate predation rates on intermediate phenotypes relative to cryptic and mimetic phenotypes under conditions of both high- and low-model abundances. Our results indicate that where coral snakes are rare, intermediate phenotypes are attacked more often than cryptic and mimetic phenotypes, indicating the presence of an adaptive valley. However, where coral snakes are abundant, intermediate phenotypes are not attacked more frequently, resulting in an adaptive landscape without a valley. Thus, high-model abundance may facilitate the evolution of Batesian mimicry. PMID:19955153

  12. High-model abundance may permit the gradual evolution of Batesian mimicry: an experimental test.

    PubMed

    Kikuchi, David W; Pfennig, David W

    2010-04-07

    In Batesian mimicry, a harmless species (the 'mimic') resembles a dangerous species (the 'model') and is thus protected from predators. It is often assumed that the mimetic phenotype evolves from a cryptic phenotype, but it is unclear how a population can transition through intermediate phenotypes; such intermediates may receive neither the benefits of crypsis nor mimicry. Here, we ask if selection against intermediates weakens with increasing model abundance. We also ask if mimicry has evolved from cryptic phenotypes in a mimetic clade. We first present an ancestral character-state reconstruction showing that mimicry of a coral snake (Micrurus fulvius) by the scarlet kingsnake (Lampropeltis elapsoides) evolved from a cryptic phenotype. We then evaluate predation rates on intermediate phenotypes relative to cryptic and mimetic phenotypes under conditions of both high- and low-model abundances. Our results indicate that where coral snakes are rare, intermediate phenotypes are attacked more often than cryptic and mimetic phenotypes, indicating the presence of an adaptive valley. However, where coral snakes are abundant, intermediate phenotypes are not attacked more frequently, resulting in an adaptive landscape without a valley. Thus, high-model abundance may facilitate the evolution of Batesian mimicry.

  13. Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen.

    PubMed

    McGovern, Emily; McCabe, Matthew S; Cormican, Paul; Popova, Milka; Keogh, Kate; Kelly, Alan K; Kenny, David A; Waters, Sinead M

    2017-10-12

    Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal's compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH 4 mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.

  14. Vegaviidae, a new clade of southern diving birds that survived the K/T boundary

    NASA Astrophysics Data System (ADS)

    Agnolín, Federico L.; Egli, Federico Brissón; Chatterjee, Sankar; Marsà, Jordi Alexis Garcia; Novas, Fernando E.

    2017-12-01

    The fossil record of Late Cretaceous-Paleogene modern birds in the Southern Hemisphere includes the Maastrichtian Neogaeornis wetzeli from Chile, Polarornis gregorii and Vegavis iaai from Antarctica, and Australornis lovei from the Paleogene of New Zealand. The recent finding of a new and nearly complete Vegavis skeleton constitutes the most informative source for anatomical comparisons among Australornis, Polarornis, and Vegavis. The present contribution includes, for the first time, Vegavis, Polarornis, and Australornis in a comprehensive phylogenetic analysis. This analysis resulted in the recognition of these taxa as a clade of basal Anseriformes that we call Vegaviidae. Vegaviids share a combination of characters related to diving adaptations, including compact and thickened cortex of hindlimb bones, femur with anteroposteriorly compressed and bowed shaft, deep and wide popliteal fossa delimited by a medial ridge, tibiotarsus showing notably proximally expanded cnemial crests, expanded fibular crest, anteroposterior compression of the tibial shaft, and a tarsometatarsus with a strong transverse compression of the shaft. Isolated bones coming from the Cretaceous and Paleogene of South America, Antarctica, and New Zealand are also referred to here to Vegaviidae and support the view that these basal anseriforms were abundant and diverse at high southern latitudes. Moreover, vegaviids represent the first avian lineage to have definitely crossed the K-Pg boundary, supporting the idea that some avian clades were not affected by the end Mesozoic mass extinction event, countering previous interpretations. Recognition of Vegaviidae indicates that modern birds were diversified in southern continents by the Cretaceous and reinforces the hypothesis indicating the important role of Gondwana for the evolutionary history of Anseriformes and Neornithes as a whole.

  15. Effect of Salt on the Metabolism of ‘Candidatus Accumulibacter’ Clade I and II

    PubMed Central

    Wang, Zhongwei; Dunne, Aislinn; van Loosdrecht, Mark C. M.; Saikaly, Pascal E.

    2018-01-01

    Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, ‘Candidatus Accumulibacter phosphatis’ Clade I and II (hereafter referred to as PAOI and PAOII) were highly enriched (∼90% in relative abundance as determined by quantitative FISH) in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P) and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5–6% at 0.256 mol/L NaCl or KCl) while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29–30% at 0.256 mol/L NaCl or KCl). In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K+) and sodium (Na+) ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance. PMID:29616002

  16. Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues

    PubMed Central

    Gao, Guangping; Vandenberghe, Luk H.; Alvira, Mauricio R.; Lu, You; Calcedo, Roberto; Zhou, Xiangyang; Wilson, James M.

    2004-01-01

    The potential for using Adeno-associated virus (AAV) as a vector for human gene therapy has stimulated interest in the Dependovirus genus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors. PMID:15163731

  17. Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex.

    PubMed

    Johnson, Jason A; Harrington, Thomas C; Engelbrecht, C J B

    2005-01-01

    Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C

  18. Nekton communities in Hawaiian coastal wetlands: The distribution and abundance of introduced fish species

    Treesearch

    Richard Ames MacKenzie; Gregory L. Bruland

    2012-01-01

    Nekton communities were sampled from 38 Hawaiian coastal wetlands from 2007 to 2009 using lift nets, seines, and throw nets in an attempt to increase our understanding of the nekton assemblages that utilize these poorly studied ecosystems. Nekton were dominated by exotic species, primarily poeciliids (Gambusia affinis, Poecilia...

  19. At-sea distribution and abundance of seabirds off southern California: A 20-year comparison

    USGS Publications Warehouse

    Mason, J.W.; McChesney, G.J.; McIver, W.R.; Carter, H.R.; Takekawa, John Y.; Golightly, R.T.; Ackerman, Joshua T.; Orthmeyer, D.L.; Perry, W.M.; Yee, J.L.; Pierson, M.O.; McCrary, M.D.

    2007-01-01

    We conducted aerial at-sea and coastal surveys to examine the distribution and abundance of seabirds off southern California, from Cambria, California, to the Mexican border. From May 1999-January 2002, we flew 102 d, covered >54,640 km of transect lines, and conducted nine complete surveys of southern California in January, May, and September. We identified 54 species comprising 12 families and counted >135,000 individuals. Seabird densities were greater along island and mainland coastlines than at sea and were usually greatest in January surveys. Densities were greatest at sea near the northern Channel Islands in January and north of Point Conception in May, and lowest in the southwestern portion of the Southern California Bight in all survey months. On coastal transects, seabird densities were greatest along central and southern portions of the mainland coastline from Point Arguello to Mexico. We estimated that 981,000 ?? 144,000 (x?? ?? SE) seabirds occurred in the study area in January, 862,000 ?? 95,000 in May, and 762,000 ?? 72,000 in September. California Gulls (Larus californicus), Western Grebes (Aechmophorus occidentalis), and Cassin's Auklets (Ptychoramphus aleuticus) were most abundant in January surveys at sea, whereas Sooty and Short-tailed shearwaters (Puffinus griseus and P. tenuirostris), phalaropes (Phalaropus spp.), and Western Gulls (Larus. occidentalis) were most abundant in May and September surveys. On coastal transects, California Gulls, Western Grebes, Western Gulls, and Surf Scoters (Melanitta perspicillata) were most abundant in January; Western Grebes, Western Gulls, Surf Scoters, and Brown Pelicans (Pelecanus occidentalis) were most abundant in May; and Sooty Shearwaters, Short-tailed Shearwaters, Western Gulls, Western Grebes, Brown Pelicans, and Heermann's Gulls (Larus heermanni) were most abundant in September. Compared to historical seabird densities collected in the same area two decades ago (1975-1978 and 1980-1983), abundance

  20. Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III.

    PubMed

    Kittichotirat, Weerayuth; Patumcharoenpol, Preecha; Rujirawat, Thidarat; Lohnoo, Tassanee; Yingyong, Wanta; Krajaejun, Theerapong

    2017-12-01

    Pythium insidiosum is a unique oomycete microorganism, capable of infecting humans and animals. The organism can be phylogenetically categorized into three distinct clades: Clade-I (strains from the Americas); Clade-II (strains from Asia and Australia), and Clade-III (strains from Thailand and the United States). Two draft genomes of the P. insidiosum Clade-I strain CDC-B5653 and Clade-II strain Pi-S are available in the public domain. The genome of P. insidiosum from the distinct Clade-III, which is distantly-related to the other two clades, is lacking. Here, we report the draft genome sequence of the P. insidiosum strain Pi45 (also known as MCC13; isolated from a Thai patient with pythiosis; accession numbers BCFM01000001-BCFM01017277) as a representative strain of the phylogenetically-distinct Clade-III. We also report a genome-scale data set of sequence variants (i.e., SNPs and INDELs) found in P. insidiosum (accessible online at the Mendeley database: http://dx.doi.org/10.17632/r75799jy6c.1).

  1. Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

    PubMed

    Song, Ha Yeun; Mabuchi, Kohji; Satoh, Takashi P; Moore, Jon A; Yamanoue, Yusuke; Miya, Masaki; Nishida, Mutsumi

    2014-06-01

    Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Revision of the Lima clade (Miconia sect. Lima, Miconieae, Melastomataceae) of the Greater Antilles

    PubMed Central

    Majure, Lucas C.; Bécquer, Eldis R.; Judd, Walter S.

    2016-01-01

    Abstract Miconia sect. Lima is an entirely Greater Antillean clade that consists of 19 known species of shrubs and small trees, which were previously recognized under the polyphyletic genera Leandra and Ossaea. The highest species richness in the clade is represented on Cuba (10 species), followed by Hispaniola (8 species) and then Jamaica (1 species). Here we present a taxonomic revision of the clade based on the study of species in the field, herbarium specimens, as well as a DNA-based phylogeny reconstruction. The Lima clade most likely originated on Cuba and then spread to Jamaica once and Hispaniola multiple times. Species of this clade can be recognized by the well developed bulla-based hairs of the adaxial leaf surface, as well as the clavate-dendritic hairs produced along the primary, secondary and tertiary veins of the adaxial leaf surface, mostly towards the leaf base, terminal inflorescences, acute petal apices, slightly bulla-based hairs produced subapically along the petal abaxial surface, and anthers with a dorso-basal appendage and a single, dorsally oriented pore. Descriptions, synonymies, along with distribution maps and illustrations/figures, are given for each species. Miconia pagnolensis sp. nov. is newly described in this revision. PMID:27829802

  3. Postantifungal effect of caspofungin against the Candida albicans and Candida parapsilosis clades.

    PubMed

    Gil-Alonso, Sandra; Jauregizar, Nerea; Eraso, Elena; Quindós, Guillermo

    2016-10-01

    Killing and postantifungal effects could be relevant for the selection of optimal dosing schedules. This study aims to compare time-kill and postantifungal effects with caspofungin on Candida albicans (C. albicans, Candida dubliniensis, Candida africana) and Candida parapsilosis (C. parapsilosis, Candida metapsilosis, Candida orthopsilosis) clades. In the postantifungal effect experiments, strains were exposed to caspofungin for 1 h at concentrations 0.12-8 μg/mL. Time-kill experiments were conducted at the same concentrations. Caspofungin exhibited a significant and prolonged postantifungal effect (>37 h) with 2 μg/mL against the most strains of C. albicans clade. Against the C. parapsilosis clade, the postantifungal effect was <12 h at 8 μg/mL, except for two strains. Caspofungin was fungicidal against C. albicans, C. dubliniensis and C. metapsilosis. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Phytoplankton biomass and microbial abundances during the spring upwelling season in the coastal area off Concepción, central-southern Chile: Variability around a time series station

    NASA Astrophysics Data System (ADS)

    Morales, Carmen E.; Anabalón, Valeria

    2012-01-01

    In the coastal system off Concepción, time series observations at a fixed station (St. 18) have shown strong seasonal changes in the oceanographic environment of the upper layer (<35 m depth), accompanied by large increases in phytoplankton biomass during the spring-summer upwelling season. These blooms, dominated by microplanktonic diatoms, have usually overshadowed the relevance of the smaller microbial components during upwelling. This study focuses on the variability of oceanographic conditions and their association with the structure of the planktonic community (size fractionated chlorophyll-a and microbial abundances) in the upper layer during the upwelling season, examining the extent to which St. 18 is representative of the coastal system off Concepción during springtime. For this purpose, data from three consecutive springs (2004, 2005, 2006) were compared, which included cruises for all years (8 stations around St. 18) as well as monthly sampling at St. 18. Most of the spatial (submesoscale) variability in chlorophyll-a and the microbial components was not significant, but data dispersion around mean values was high. Water column structure (temperature and salinity) in the upper layer explained a significant fraction (25-65%) of the spatial variability in most of the planktonic components; their responses to oceanographic variability were linear in some cases and non-linear in others. For the most part, St. 18 appears to adequately represent mean oceanographic conditions and the structure of planktonic communities in the coastal waters off Concepción during springtime, however spatial variability needs to be taken into account in the interpretations of temporal changes at this fixed station as well as in assessments of carbon flow within, and exportation processes from, this upwelling system.

  5. An Anti-HIV-1 V3 Loop Antibody Fully Protects Cross-Clade and Elicits T-Cell Immunity in Macaques Mucosally Challenged with an R5 Clade C SHIV

    PubMed Central

    Lakhashe, Samir K.; Humbert, Michael; Sholukh, Anton; Hemashettar, Girish; Wong, Yin Ling; Yoon, John K.; Wang, Wendy; Novembre, Francis J.; Villinger, Francois; Ibegbu, Chris; Patel, Kalpana; Corti, Davide; Agatic, Gloria; Vanzetta, Fabrizia; Bianchi, Siro; Heeney, Jonathan L.; Sallusto, Federica; Lanzavecchia, Antonio; Ruprecht, Ruth M.

    2011-01-01

    Neutralizing antibodies have been shown to protect macaques against SHIV challenge. However, genetically diverse HIV-1 clades have evolved, and a key question left unanswered is whether neutralizing antibodies can confer cross-clade protection in vivo. The novel human monoclonal antibody HGN194 was isolated from an individual infected with an HIV-1 clade AG recombinant circulating recombinant form (CRF). HGN194 targets an epitope in the third hypervariable loop (V3) of HIV-1 gp120 and neutralizes a range of relatively neutralization-sensitive and resistant viruses. We evaluated the potential of HGN194 to protect infant rhesus monkeys against a SHIV encoding a primary CCR5-tropic HIV-1 clade C envelope. After high-dose mucosal challenge, all untreated controls became highly viremic while all HGN194-treated animals (50 mg/kg) were completely protected. When HGN194 was given at 1 mg/kg, one out of two monkeys remained aviremic, whereas the other had delayed, lower peak viremia. Interestingly, all protected monkeys given high-dose HGN194 developed Gag-specific proliferative responses of both CD4+ and CD8+ T cells. To test whether generation of the latter involved cryptic infection, we ablated CD8+ cells after HGN194 clearance. No viremia was detected in any protected monkeys, thus ruling out virus reservoirs. Thus, induction of CD8 T-cell immunity may have resulted from transient “Hit and Run” infection or cross priming via Ag-Ab-mediated cross-presentation. Together, our data identified the HGN194 epitope as protective and provide proof-of-concept that this anti-V3 loop mAb can prevent infection with sterilizing immunity after challenge with virus of a different clade, implying that V3 is a potential vaccine target. PMID:21483815

  6. Anuran trypanosomes: phylogenetic evidence for new clades in Brazil.

    PubMed

    da S Ferreira, Juliana I G; da Costa, Andrea P; Ramirez, Diego; Roldan, Jairo A M; Saraiva, Danilo; da S Founier, Gislene F R; Sue, Ana; Zambelli, Erick R; Minervino, Antonio H H; Verdade, Vanessa K; Gennari, Solange M; Marcili, Arlei

    2015-05-01

    Trypanosomes of anurans and fish are grouped into the Aquatic Clade which includes species isolated from fish, amphibians, turtles and platypus, usually transmitted by leeches and phlebotomine sand flies. Trypanosomes from Brazilian frogs are grouped within the Aquatic Clade with other anuran trypanosome species, where there seems to be coevolutionary patterns with vertebrate hosts and association to Brazilian biomes (Atlantic Forest, Pantanal and Amazonia Rainforest). We characterised the anuran trypanosomes from two different areas of the Cerrado biome and examined their phylogenetic relationships based on the SSU rRNA gene. A total of 112 anurans of six species was analysed and trypanosome prevalence evaluated through haemoculture was found to be 7% (8 positive frogs). However, only three isolates (2.7%) from two anuran species were recovered and cryopreserved. Analysis including SSU rDNA sequences from previous studies segregated the anuran trypanosomes into six groups, the previously reported An01 to An04, and An05 and An06 reported herein. Clade An05 comprises the isolates from Leptodactylus latrans (Steffen) and Pristimantis sp. captured in the Cerrado biome and Trypanosoma chattoni Mathis & Leger, 1911. The inclusion of new isolates in the phylogenetic analyses provided evidence for a new group (An06) of parasites from phlebotomine hosts. Our results indicate that the diversity of trypanosome species is underestimated since studies conducted in Brazil and other regions of the world are still few.

  7. Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota

    USDA-ARS?s Scientific Manuscript database

    The species boundaries of wild and cultivated potatoes, Solanum section Petota, are controversial with most of the taxonomic problems in a clade containing cultivated potatoes. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these pr...

  8. Spatial and temporal variations of urban litter in Mar del Plata, the major coastal city of Argentina.

    PubMed

    Seco Pon, Juan Pablo; Becherucci, Maria Eugenia

    2012-02-01

    Urban littering is considered an important environmental and public issue globally. This problem is growing considerably within coastal communities of the southern region of South America. The goals of this study were to assess (1) the abundance and composition of urban litter; (2) the spatial and temporal variations of its abundance; and (3) the relationship between the abundance of litter and three anthropogenic variables (i.e. abundance of pedestrians, of parked vehicles, and of trash bins) in Mar del Plata, the most populated coastal city in Argentina. Eighty-eight transects, each covering 1425 m(2), were sampled along four sites from April 2008 to March 2009. Results showed 20,336 items (ca. 14 items per m(2)) of which cigarette butts (33%), papers (31%), and plastics (22%) were the most commonly littered items. Higher amounts of litter were found in an industrial area (city's harbor), while the abundance of litter appeared relatively even throughout the year. Redundancy analysis techniques indicated a high abundance of all three anthropogenic variables associated with the central business district area of the city and an area in close proximity to a major seaside resort, where cigarette butts and papers dominated. This is the first study that has examined spatial and temporal variations of urban litter in a high-density coastal city in Argentina. Our results showed that addressing the problems associated with urban litter must include intensive educational and advertising campaigns directed at pedestrians and owners of parked vehicles, but waste reduction, clean-up operations and law enforcement should be also considered. Copyright © 2011. Published by Elsevier Ltd.

  9. Coastal Upwelling Drives Intertidal Assemblage Structure and Trophic Ecology

    PubMed Central

    Reddin, Carl J.; Docmac, Felipe; O’Connor, Nessa E.; Bothwell, John H.; Harrod, Chris

    2015-01-01

    Similar environmental driving forces can produce similarity among geographically distant ecosystems. Coastal oceanic upwelling, for example, has been associated with elevated biomass and abundance patterns of certain functional groups, e.g., corticated macroalgae. In the upwelling system of Northern Chile, we examined measures of intertidal macrobenthic composition, structure and trophic ecology across eighteen shores varying in their proximity to two coastal upwelling centres, in a hierarchical sampling design (spatial scales of >1 and >10 km). The influence of coastal upwelling on intertidal communities was confirmed by the stable isotope values (δ13C and δ15N) of consumers, including a dominant suspension feeder, grazers, and their putative resources of POM, epilithic biofilm, and macroalgae. We highlight the utility of muscle δ15N from the suspension feeding mussel, Perumytilus purpuratus, as a proxy for upwelling, supported by satellite data and previous studies. Where possible, we used corrections for broader-scale trends, spatial autocorrelation, ontogenetic dietary shifts and spatial baseline isotopic variation prior to analysis. Our results showed macroalgal assemblage composition, and benthic consumer assemblage structure, varied significantly with the intertidal influence of coastal upwelling, especially contrasting bays and coastal headlands. Coastal topography also separated differences in consumer resource use. This suggested that coastal upwelling, itself driven by coastline topography, influences intertidal communities by advecting nearshore phytoplankton populations offshore and cooling coastal water temperatures. We recommend the isotopic values of benthic organisms, specifically long-lived suspension feeders, as in situ alternatives to offshore measurements of upwelling influence. PMID:26214806

  10. Structure of Mesozooplankton Communities in the Coastal Waters of Morocco

    NASA Astrophysics Data System (ADS)

    Lidvanov, V. V.; Grabko, O. G.; Kukuev, E. I.; Korolkova, T. G.

    2018-03-01

    Mero- and holoplanktonic organisms from 23 large taxa have been detected in the coastal waters of Morocco. Seven Cladocera species and 164 Copepoda species were identified. Copepod fauna mostly consisted of oceanic epipelagic widely tropical species, but the constant species group (frequency of occurrence over 50%) included neritic and neritic-oceanic widely tropical species. The neritic community that formed a biotopic association with coastal upwelling waters and the distant-neritic community associated with Canary Current waters were the two major communities detected. The former community was characterized by a high abundance and biomass (5700 ind./m3 and 260 mg/m3) and predominance of neritic species. The trophic structure was dominated by thin filter feeders, mixed-food consumers, and small grabbers; the species structure was dominated by Paracalanus indicus, Acartia clausi, and Oncaea curta; the indices of species diversity (3.07 bit/ind.) and evenness (0.63) were relatively low. The latter community was characterized by low abundance and biomass (1150 ind./m3 and 90 mg/m3); variable biotopic, trophic, and species structure; and higher Shannon indices (3.99 bit/ind.) and Pielou (0.75). Seasonal variation of the abundance of organisms was not detected in the communities. Anomalous mesozooplankton states were observed in summer 1998 and winter 1998-1999.

  11. Cyanobacterial distributions along a physico-chemical gradient in the Northeastern Pacific Ocean.

    PubMed

    Sudek, Sebastian; Everroad, R Craig; Gehman, Alyssa-Lois M; Smith, Jason M; Poirier, Camille L; Chavez, Francisco P; Worden, Alexandra Z

    2015-10-01

    The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and covariance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. An inter-annual pattern was delineated in the dynamic transition zone where upwelled and eastern boundary current waters mix, and two new Synechococcus clades, Eastern Pacific Clade (EPC) 1 and EPC2, were identified. By applying state-of-the-art phylogenetic analysis tools to bar-coded 16S amplicon datasets, we observed higher abundance of Prochlorococcus high-light I (HLI) and low-light I (LLI) in years when more oligotrophic water intruded farther inshore, while under stronger upwelling Synechococcus I and IV dominated. However, contributions of some cyanobacterial clades were proportionally relatively constant, e.g. Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than previously reported. The phylogenetic precision of our 16S rRNA gene analytical approach and depth of bar-coded sequencing also facilitated detection of clades at low abundance in unexpected places. These include Prochlorococcus at the coast and Cyanobium-related sequences offshore, although it remains unclear whether these came from resident or potentially advected cells. Our study enhances understanding of cyanobacterial distributions in an ecologically important eastern boundary system. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  12. Factors regulating early life history dispersal of Atlantic cod (Gadus morhua) from coastal Newfoundland.

    PubMed

    Stanley, Ryan R E; deYoung, Brad; Snelgrove, Paul V R; Gregory, Robert S

    2013-01-01

    To understand coastal dispersal dynamics of Atlantic cod (Gadus morhua), we examined spatiotemporal egg and larval abundance patterns in coastal Newfoundland. In recent decades, Smith Sound, Trinity Bay has supported the largest known overwintering spawning aggregation of Atlantic cod in the region. We estimated spawning and dispersal characteristics for the Smith Sound-Trinity Bay system by fitting ichthyoplankton abundance data to environmentally-driven, simplified box models. Results show protracted spawning, with sharply increased egg production in early July, and limited dispersal from the Sound. The model for the entire spawning season indicates egg export from Smith Sound is 13%•day(-1) with a net mortality of 27%•day(-1). Eggs and larvae are consistently found in western Trinity Bay with little advection from the system. These patterns mirror particle tracking models that suggest residence times of 10-20 days, and circulation models indicating local gyres in Trinity Bay that act in concert with upwelling dynamics to retain eggs and larvae. Our results are among the first quantitative dispersal estimates from Smith Sound, linking this spawning stock to the adjacent coastal waters. These results illustrate the biophysical interplay regulating dispersal and connectivity originating from inshore spawning of coastal northwest Atlantic.

  13. Factors Regulating Early Life History Dispersal of Atlantic Cod (Gadus morhua) from Coastal Newfoundland

    PubMed Central

    Stanley, Ryan R. E.; deYoung, Brad; Snelgrove, Paul V. R.; Gregory, Robert S.

    2013-01-01

    To understand coastal dispersal dynamics of Atlantic cod (Gadus morhua), we examined spatiotemporal egg and larval abundance patterns in coastal Newfoundland. In recent decades, Smith Sound, Trinity Bay has supported the largest known overwintering spawning aggregation of Atlantic cod in the region. We estimated spawning and dispersal characteristics for the Smith Sound-Trinity Bay system by fitting ichthyoplankton abundance data to environmentally-driven, simplified box models. Results show protracted spawning, with sharply increased egg production in early July, and limited dispersal from the Sound. The model for the entire spawning season indicates egg export from Smith Sound is 13%•day−1 with a net mortality of 27%•day–1. Eggs and larvae are consistently found in western Trinity Bay with little advection from the system. These patterns mirror particle tracking models that suggest residence times of 10–20 days, and circulation models indicating local gyres in Trinity Bay that act in concert with upwelling dynamics to retain eggs and larvae. Our results are among the first quantitative dispersal estimates from Smith Sound, linking this spawning stock to the adjacent coastal waters. These results illustrate the biophysical interplay regulating dispersal and connectivity originating from inshore spawning of coastal northwest Atlantic. PMID:24058707

  14. Coastal regime shifts: rapid responses of coastal wetlands to changes in mangrove cover.

    PubMed

    Guo, Hongyu; Weaver, Carolyn; Charles, Sean P; Whitt, Ashley; Dastidar, Sayantani; D'Odorico, Paolo; Fuentes, Jose D; Kominoski, John S; Armitage, Anna R; Pennings, Steven C

    2017-03-01

    Global changes are causing broad-scale shifts in vegetation communities worldwide, including coastal habitats where the borders between mangroves and salt marsh are in flux. Coastal habitats provide numerous ecosystem services of high economic value, but the consequences of variation in mangrove cover are poorly known. We experimentally manipulated mangrove cover in large plots to test a set of linked hypotheses regarding the effects of changes in mangrove cover. We found that changes in mangrove cover had strong effects on microclimate, plant community, sediment accretion, soil organic content, and bird abundance within 2 yr. At higher mangrove cover, wind speed declined and light interception by vegetation increased. Air and soil temperatures had hump-shaped relationships with mangrove cover. The cover of salt marsh plants decreased at higher mangrove cover. Wrack cover, the distance that wrack was distributed from the water's edge, and sediment accretion decreased at higher mangrove cover. Soil organic content increased with mangrove cover. Wading bird abundance decreased at higher mangrove cover. Many of these relationships were non-linear, with the greatest effects when mangrove cover varied from zero to intermediate values, and lesser effects when mangrove cover varied from intermediate to high values. Temporal and spatial variation in measured variables often peaked at intermediate mangrove cover, with ecological consequences that are largely unexplored. Because different processes varied in different ways with mangrove cover, the "optimum" cover of mangroves from a societal point of view will depend on which ecosystem services are most desired. © 2016 by the Ecological Society of America.

  15. Infection of Monkeys by Simian-human Immunodeficiency Viruses with Transmitted/ founder Clade C HIV-1 Envelopes

    PubMed Central

    Asmal, Mohammed; Luedemann, Corinne; Lavine, Christy L.; Mach, Linh V.; Balachandran, Harikrishnan; Brinkley, Christie; Denny, Thomas N.; Lewis, Mark G.; Anderson, Hanne; Pal, Ranajit; Sok, Devin; Le, Khoa; Pauthner, Matthias; Hahn, Beatrice H.; Shaw, George M.; Seaman, Michael S.; Letvin, Norman L.; Burton, Dennis R.; Sodroski, Joseph G.; Haynes, Barton F.; Santra, Sampa

    2014-01-01

    Simian-human immunodeficiency viruses (SHIVs) that mirror natural transmitted/founder (T/F) viruses in man are needed for evaluation of HIV-1 vaccine candidates in nonhuman primates. Currently available SHIVs contain HIV-1 env genes from chronically-infected individuals and do not reflect the characteristics of biologically relevant HIV-1 strains that mediate human transmission. We chose to develop clade C SHIVs, as clade C is the major infecting subtype of HIV-1 in the world. We constructed ten clade C SHIVs expressing Env proteins from T/F viruses. Three of these ten clade C SHIVs (SHIV KB9 C3, SHIV KB9 C4 and SHIV KB9 C5) replicated in naïve rhesus monkeys. These three SHIVs are mucosally transmissible and are neutralized by sCD4 and several HIV-1 broadly neutralizing antibodies. However, like natural T/F viruses, they exhibit low Env reactivity and a Tier 2 neutralization sensitivity. Of note, none of the clade C T/F SHIVs elicited detectable autologous neutralizing antibodies in the infected monkeys, even though antibodies that neutralized a heterologous Tier 1 HIV-1 were generated. Challenge with these three new clade C SHIVs will provide biologically relevant tests for vaccine protection in rhesus macaques. PMID:25462344

  16. Efficacy of clade 2.3.2 H5 commercial vaccines in protecting chickens from clade 2.3.4.4 H5N8 highly pathogenic avian influenza infection.

    PubMed

    Yuk, Seong-Su; Erdene-Ochir, T O; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-Tack; Jeong, Jei-Hyun; Jeong, Sol; Gwon, Gyeong-Bin; Shin, Jong-Il; Sur, Jung-Hyang; Song, Chang-Seon

    2017-03-01

    Emerging clade 2.3.4.4 of the highly pathogenic avian influenza (HPAI) virus strain H5N8, which had been detected sporadically in domestic poultry in China, started to affect wild birds and poultry in South Korea in 2014. The virus was spread to Germany, Italy, the Netherlands, United Kingdom, and even United States by migratory birds. Here, we tested currently used commercial clade 2.3.2 H5 vaccines to evaluate mortality, clinical signs, virus shedding, and histological damage after experimental infection of chickens with the clade 2.3.4.4 HPAI H5N8 virus. Although the vaccination protected chickens from death, it failed to prevent chickens from shedding the virus and from tissue damage according to histological examination. These results suggest that the use of appropriate vaccines that match the currently epidemic HPAI virus is recommended, and continuous HPAI surveillance and testing of currently used commercial vaccines should be performed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Coastal Wetland Ecosystem Responses to Climate Change: the Role of Macroclimatic Drivers along the Northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Osland, M. J.; Enwright, N.; Day, R. H.; Gabler, C. A.; Stagg, C. L.; From, A. S.

    2014-12-01

    Across the globe, macroclimatic drivers greatly influence coastal wetland ecosystem structure and function. However, changing macroclimatic conditions are rarely incorporated into coastal wetland vulnerability assessments. Here, we quantify the influence of macroclimatic drivers upon coastal wetland ecosystems along the Northern Gulf of Mexico (NGOM) coast. From a global perspective, the NGOM coast provides several excellent opportunities to examine the effects of climate change upon coastal wetlands. The abundant coastal wetland ecosystems in the region span two major climatic gradients: (1) a winter temperature gradient that crosses temperate to tropical climatic zones; and (2) a precipitation gradient that crosses humid to semi-arid zones. We present analyses where we used geospatial data (historical climate, hydrology, and coastal wetland coverage) and field data (soil, elevation, and plant community composition and structure) to quantify climate-mediated ecological transitions. We identified winter climate and precipitation-based thresholds that separate mangrove forests from salt marshes and vegetated wetlands from unvegetated wetlands, respectively. We used simple distribution and abundance models to evaluate the potential ecological effects of alternative future climate change scenarios. Our results illustrate and quantify the importance of macroclimatic drivers and indicate that climate change could result in landscape-scale changes in coastal wetland ecosystem structure and function. These macroclimate-mediated ecological changes could affect the supply of some ecosystem goods and services as well as the resilience of these ecosystems to stressors, including accelerated sea level rise. Collectively, our findings highlight the importance of incorporating macroclimatic drivers within future-focused coastal wetland vulnerability assessments.

  18. Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean

    PubMed Central

    Suzuki, Shotaro; Omori, Yuko; Wong, Shu-Kuan; Ijichi, Minoru; Kaneko, Ryo; Kameyama, Sohiko; Tanimoto, Hiroshi; Hamasaki, Koji

    2015-01-01

    Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean. PMID:25862229

  19. Abundance and distribution of dimethylsulfoniopropionate degradation genes and the corresponding bacterial community structure at dimethyl sulfide hot spots in the tropical and subtropical pacific ocean.

    PubMed

    Cui, Yingshun; Suzuki, Shotaro; Omori, Yuko; Wong, Shu-Kuan; Ijichi, Minoru; Kaneko, Ryo; Kameyama, Sohiko; Tanimoto, Hiroshi; Hamasaki, Koji

    2015-06-15

    Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  20. A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica.

    PubMed

    Ortiz-Rodriguez, Andrés Ernesto; Ornelas, Juan Francisco; Ruiz-Sanchez, Eduardo

    2018-05-01

    The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions. Copyright © 2018 Elsevier Inc. All rights

  1. Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate

    PubMed Central

    2013-01-01

    Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity. PMID:23835244

  2. Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate.

    PubMed

    Visciano, Maria Luisa; Tagliamonte, Maria; Stewart-Jones, Guillaume; Heyndrickx, Leo; Vanham, Guido; Jansson, Marianne; Fomsgaard, Anders; Grevstad, Berit; Ramaswamy, Meghna; Buonaguro, Franco M; Tornesello, Maria Lina; Biswas, Priscilla; Scarlatti, Gabriella; Buonaguro, Luigi

    2013-07-08

    Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity.

  3. Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade

    Treesearch

    Karl-Henrik Larsson; Erast Parmasto; Michael Fischer; Ewald Langer; Karen K. Nakasone; Scott A. Redhead

    2006-01-01

    The hymenochaetoid clade is dominated by wood-decaying species previously classified in the artificial families Corticiaceae, Polyporaceae and Stereaceae. The majority of these species cause a white rot. The polypore Bridgeoporus and several corticioid species with inconspicuous basidiomata live in association with brown-rotted wood, but their nutritional strategy is...

  4. Seasonal variation in natural abundance of δ13C and 15N in Salicornia brachiata Roxb. populations from a coastal area of India.

    PubMed

    Chaudhary, Doongar R; Seo, Juyoung; Kang, Hojeong; Rathore, Aditya P; Jha, Bhavanath

    2018-05-01

    High and fluctuating salinity is characteristic for coastal salt marshes, which strongly affect the physiology of halophytes consequently resulting in changes in stable isotope distribution. The natural abundance of stable isotopes (δ 13 C and δ 15 N) of the halophyte plant Salicornia brachiata and physico-chemical characteristics of soils were analysed in order to investigate the relationship of stable isotope distribution in different populations in a growing period in the coastal area of Gujarat, India. Aboveground and belowground biomass of S. brachiata was collected from six different populations at five times (September 2014, November 2014, January 2015, March 2015 and May 2015). The δ 13 C values in aboveground (-30.8 to -23.6 ‰, average: -26.6 ± 0.4 ‰) and belowground biomass (-30.0 to -23.1 ‰, average: -26.3 ± 0.4 ‰) were similar. The δ 13 C values were positively correlated with soil salinity and Na concentration, and negatively correlated with soil mineral nitrogen. The δ 15 N values of aboveground (6.7-16.1 ‰, average: 9.6 ± 0.4 ‰) were comparatively higher than belowground biomass (5.4-13.2 ‰, average: 7.8 ± 0.3 ‰). The δ 15 N values were negatively correlated with soil available P. We conclude that the variation in δ 13 C values of S. brachiata was possibly caused by soil salinity (associated Na content) and N limitation which demonstrates the potential of δ 13 C as an indicator of stress in plants.

  5. HIV-1 Gp120 clade B/C induces a GRP78 driven cytoprotective mechanism in astrocytoma

    PubMed Central

    López, Sheila N.; Rodríguez-Valentín, Madeline; Rivera, Mariela; Rodríguez, Maridaliz; Babu, Mohan; Cubano, Luis A.; Xiong, Huangui; Wang, Guangdi; Kucheryavykh, Lilia; Boukli, Nawal M.

    2017-01-01

    HIV-1 clades are known to be one of the key factors implicated in modulating HIV-associated neurocognitive disorders. HIV-1 B and C clades account for the majority of HIV-1 infections, clade B being the most neuropathogenic. The mechanisms behind HIV-mediated neuropathogenesis remain the subject of active research. We hypothesized that HIV-1 gp120 clade B and C proteins may exert differential proliferation, cell survival and NeuroAIDS effects in human astrocytoma cells via the Unfolded Protein Response, an endoplasmic reticulum- based cytoprotective mechanism. The differential effect of gp120 clade B and C was evaluated using for the first time a Tandem Mass Tag isobaric labeling quantitative proteomic approach. Flow cytometry analyses were performed for cell cycle and cell death identification. Among the proteins differentiated by HIV-1 gp120 proteins figure cytoskeleton, oxidative stress, UPR markers and numerous glycolytic metabolism enzymes. Our results demonstrate that HIV-1 gp120 B induced migration, proliferative and protective responses granted by the expression of GRP78, while HIV-1 gp120 C induced the expression of key inflammatory and pro-apoptotic markers. These novel findings put forward the first evidence that GRP78 is a key player in HIV-1 clade B and C neuropathogenic discrepancies and can be used as a novel target for immunotherapies. PMID:28978127

  6. Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

    PubMed

    Liu, Xiu-Qun; Ickert-Bond, Stefanie M; Nie, Ze-Long; Zhou, Zhuo; Chen, Long-Qing; Wen, Jun

    2016-02-01

    The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Copyright © 2015

  7. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss.

    PubMed

    Braukmann, Thomas; Kuzmina, Maria; Stefanovic, Sasa

    2013-02-01

    The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a

  8. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    PubMed Central

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  9. Impacts of the Nutrient Inputs from Riverine on the Dynamic and Community Structure of Fungal-like Protists in the Coastal Ocean Ecosystems

    NASA Astrophysics Data System (ADS)

    Duan, Y.; Wang, G.; Xie, N.

    2016-02-01

    The coastal ocean connects terrestrial (e.g., rivers and estuaries) with oceanic ecosystems and is considered as a major component of global carbon cycles and budgets. The coastal waters are featured with a high biodiversity and high primary production. Because of the excessive primary production, a large fraction of primary organic matter becomes available to consumers as detritus in the coastal waters. Bacterioplankton have long been known to play a key role in the degradation of this detritus, and export and storage of organic matter in the coastal ecosystems. However, the primary and secondary production and the carbon biogeochemical processes in the ecosystems are largely regulated by nutrient inputs from riverine and other anthropogenic activities through heterotrophic microbial communities. Thraustochytrids, commonly known as fungal-like protists, are unicellular heterotrophic protists and are recently acknowledged to play a significant role in ocean carbon cycling. Their abundance exceeds that of bacterioplankton in the most time of the year in the coastal waters of China. Also, their abundance and diversity are largely regulated by nutrients inputs from riverine and other anthropogenic activities. Our findings support that thraustochytrids are a dominant heterotrophic microbial group in the coastal waters. Evidently, thraustochytrids are an import, but neglected, component in microbial carbon biogeochemical processes of the coastal ocean.

  10. Influence of microorganism content in suspended particles on the particle-water partitioning of mercury in semi-enclosed coastal waters.

    PubMed

    Jang, Jiyi; Kim, Hyunji; Han, Seunghee

    2014-02-01

    It is known that particle scavenging of mercury (Hg) can be affected by the abundance of particulate organic matter in coastal waters. However, the role of living organic particles in Hg scavenging is not yet completely understood. In this study, we hypothesized that an abundance of living organic particles (i.e., phytoplankton and bacteria) would influence the particle-water partitioning of Hg in coastal waters. Surface seawater samples were collected from eight stations in Gwangyang Bay, Korea, in three seasons (November 2009, April 2010, and October 2010) for the determination of concentrations of suspended particulate matter (including chlorophyll-a and bacteria), and Hg in unfiltered and filtered waters. We found that more Hg partitioned toward particulate matter when phytoplankton biomass, indicated from the chlorophyll-a concentration in a particle, was higher. In the low algal season, when [chlorophyll-a]<0.6 μg L(-1), the bacterial number, instead of chlorophyll-a concentration in particle, showed a positive correlation with the particle-water partition coefficient of Hg. Overall, microbial abundance seems to play a critical role in particle scavenging of Hg in coastal water. Taking this result in light of Hg in pristine coastal zones, we predict that increases in algal biomass amplify the potential for algae to transfer Hg to marine food chains. © 2013.

  11. Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

    PubMed

    Mayali, Xavier; Weber, Peter K

    2018-05-01

    To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

  12. Trading Capsule for Increased Cytotoxin Production: Contribution to Virulence of a Newly Emerged Clade of emm89 Streptococcus pyogenes.

    PubMed

    Zhu, Luchang; Olsen, Randall J; Nasser, Waleed; de la Riva Morales, Ivan; Musser, James M

    2015-10-06

    Strains of emm89 Streptococcus pyogenes have become one of the major causes of invasive infections worldwide in the last 10 years. We recently sequenced the genome of 1,125 emm89 strains and identified three major phylogenetic groups, designated clade 1, clade 2, and the epidemic clade 3. Epidemic clade 3 strains, which now cause the great majority of infections, have two distinct genetic features compared to clade 1 and clade 2 strains. First, all clade 3 organisms have a variant 3 nga promoter region pattern, which is associated with increased production of secreted cytolytic toxins SPN (S. pyogenes NADase) and SLO (streptolysin O). Second, all clade 3 strains lack the hasABC locus mediating hyaluronic acid capsule synthesis, whereas this locus is intact in clade 1 and clade 2 strains. We constructed isogenic mutant strains that produce different levels of SPN and SLO toxins and capsule (none, low, or high). Here we report that emm89 strains with elevated toxin production are significantly more virulent than low-toxin producers. Importantly, we also show that capsule production is dispensable for virulence in strains that already produce high levels of SPN and SLO. Our results provide new understanding about the molecular mechanisms contributing to the rapid emergence and molecular pathogenesis of epidemic clade 3 emm89 S. pyogenes. S. pyogenes (group A streptococcus [GAS]) causes pharyngitis ("strep throat"), necrotizing fasciitis, and other human infections. Serious infections caused by emm89 S. pyogenes strains have recently increased in frequency in many countries. Based on whole-genome sequence analysis of 1,125 strains recovered from patients on two continents, we discovered that a new emm89 clone, termed clade 3, has two distinct genetic features compared to its predecessors: (i) absence of the genes encoding antiphagocytic hyaluronic acid capsule virulence factor and (ii) increased production of the secreted cytolytic toxins SPN and SLO. emm89 S

  13. Diatom species abundance and morphologically-based dissolution proxies in coastal Southern Ocean assemblages

    NASA Astrophysics Data System (ADS)

    Warnock, Jonathan P.; Scherer, Reed P.

    2015-07-01

    Taphonomic processes alter diatom assemblages in sediments, thus potentially negatively impacting paleoclimate records at various rates across space, time, and taxa. However, quantitative taphonomic data is rarely included in diatom-based paleoenvironmental reconstructions and no objective standard exists for comparing diatom dissolution in sediments recovered from marine depositional settings, including the Southern Ocean's opal belt. Furthermore, identifying changes to diatom dissolution through time can provide insight into the efficiency of both upper water column nutrient recycling and the biological pump. This is significant in that reactive metal proxies (e.g. Al, Ti) in the sediments only account for post-depositional dissolution, not the water column where the majority of dissolution occurs. In order to assess the range of variability of responses to dissolution in a typical Southern Ocean diatom community and provide a quantitative guideline for assessing taphonomic variability in diatoms recovered from core material, a sediment trap sample was subjected to controlled, serial dissolution. By evaluating dissolution-induced changes to diatom species' relative abundance, three preservational categories of diatoms have been identified: gracile, intermediate, and robust. The relative abundances of these categories can be used to establish a preservation grade for diatom assemblages. However, changes to the relative abundances of diatom species in sediment samples may reflect taphonomic or ecological factors. In order to address this complication, relative abundance changes have been tied to dissolution-induced morphological change to the areolae of Fragilariopsis curta, a significant sea-ice indicator in Southern Ocean sediments. This correlation allows differentiation between gracile species loss to dissolution versus ecological factors or sediment winnowing. These results mirror a similar morphological dissolution index from a parallel study utilizing

  14. REMOTE DETECTION OF INVASSIVE AND OPPORTUNISTIC PLANT SPECIES IN GREAT LAKES COASTAL WETLANDS

    EPA Science Inventory

    Invasive and opportunistic plant species have been associated with wetland disturbance. Increases in the abundance of plant species such as common reed (Phragmites australis) in coastal Great Lakes wetlands are hypothesized to occur with shifts toward drier hydrologic regimes, fr...

  15. REMOTE DETENTION OF INVASIVE AND OPPORTUNISTIC PLANT SPECIES IN GREAT LAKES COASTAL WETLANDS

    EPA Science Inventory

    Invasive and opportunistic plant species have been associated with wetland disturbance. Increases in the abundance of plant species such as common reed (Phragmites australis) in coastal Great Lakes wetlands are hypothesized to occur with shifts toward drier hydrologic regimes, fr...

  16. Distribution of Vibrio alginolyticus-like species in Shenzhen coastal waters, China

    PubMed Central

    Chen, Ming-Xia; Li, He-Yang; Li, Gang; Zheng, Tian-Ling

    2011-01-01

    We investigated the distribution of vibrios in Shenzhen coastal waters in order to obtain valuable information for the aquaculture industry and a health warning system. Quantities of vibrios from surface waters ranged from 0 to 4.40×104 CFUs mL-1 in April (spring), while from 0 to 2.57×103 CFUs mL-1 in September (autumn); the abundance of V. alginolyticus-like species from surface water ranged from 0 to 6.72×103 CFUs mL-1 in April (spring) and from 0 to 1.28×103 CFUs mL-1 in September (autumn); higher counts were observed in spring. The V. alginolyticus-like species was dominant in Shenzhen coastal waters, with the highest abundance in the clean region (stations YMK001 and GDN064) in April, suggesting that Vibrio spp. were naturally occurring bacteria in marine environments. The correlation between the abundance of vibrios (including V. alginolyticus-like species) and environmental factors varied in different regions and different seasons. There were no vibrios detected when the salinity was less than 11.15‰ in the Zhujiang River estuary, which indicated that salinity played a key role in the distribution of vibrios and V. alginolyticus-like species. PMID:24031704

  17. Corallite wall and septal microstructure in scleractinian reef corals: comparison of molecular clades within the family Faviidae.

    PubMed

    Budd, Ann F; Stolarski, Jarosław

    2011-01-01

    Recent molecular phylogenies conflict with traditional scleractinian classification at ranks ranging from suborder to genus, challenging morphologists to discover new characters that better agree with molecular data. Such characters are essential for including fossils in analyses and tracing evolutionary patterns through geologic time. We examine the skeletal morphology of 36 species belonging to the traditional families Faviidae, Merulinidae, Pectiniidae, and Trachyphylliidae (3 Atlantic, 14 Indo-Pacific, 2 cosmopolitan genera) at the macromorphological, micromorphological, and microstructural levels. Molecular analyses indicate that the families are not monophyletic groups, but consist of six family-level clades, four of which are examined [clade XV = Diploastrea heliopora; clade XVI = Montastraea cavernosa; clade XVII ("Pacific faviids") = Pacific faviids (part) + merulinids (part) + pectiniids (part) + M. annularis complex; clade XXI ("Atlantic faviids") = Atlantic faviids (part) + Atlantic mussids]. Comparisons among molecular clades indicate that micromorphological and microstructural characters (singly and in combination) are clade diagnostic, but with two exceptions, macromorphologic characters are not. The septal teeth of "Atlantic faviids" are paddle-shaped (strong secondary calcification axes) or blocky, whereas the septal teeth of "Pacific faviids" are spine-shaped or multidirectional. Corallite walls in "Atlantic faviids" are usually septothecal, with occasional trabeculothecal elements; whereas corallite walls in "Pacific faviids" are usually trabeculothecal or parathecal or they contain abortive septa. Exceptions include subclades of "Pacific faviids" consisting of a) Caulastraea and Oulophyllia (strong secondary axes) and b) Cyphastrea (septothecal walls). Diploastrea has a diagnostic synapticulothecal wall and thick triangular teeth; Montastraea cavernosa is also distinct, possessing both "Pacific faviid" (abortive septa) and "Atlantic faviid

  18. Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material

    PubMed Central

    De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

    2016-01-01

    Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade. PMID:27790062

  19. Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines.

    PubMed

    Monroe, Nicole; Hill, Christopher P

    2016-05-08

    Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Lead distribution in coastal and estuarine sediments around India.

    PubMed

    Chakraborty, Sucharita; Chakraborty, Parthasarathi; Nath, B Nagender

    2015-08-15

    This study describes the geochemical distribution of lead (Pb) and identifies the critical factors that significantly control Pb distribution and speciation in coastal and estuarine sediments around India by using published data from the literature. Crustal sources influence the abundance of Pb in coastal sediment from the south-east and central-west coast of India. Parts of north-east, north-west, and south-west coast of India were polluted by Pb. Distribution of Pb in sediments, from the north-east and north-west coasts of India, were controlled by Fe-Mn oxyhydroxide mineral phases of the sediments. However, organic carbon (OC) seemed to be a dominant factor in controlling the distribution of Pb in sediments from the central-east and south-west coasts of India. The outcome of this study may help in decision-making to predict the levels of Pb from natural and anthropogenic sources and to control Pb pollution in coastal and estuarine sediments around India. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Grey mullet (Mugilidae) as possible indicators of global warming in South African estuaries and coastal waters.

    PubMed

    James, Nicola C; Whitfield, Alan K; Harrison, Trevor D

    2016-12-01

    The grey mullet usually occur in large numbers and biomass in the estuaries of all three South African biogeographic regions, thus making it an ideal family to use in terms of possibly acting as an environmental indicator of global warming. In this analysis the relative estuarine abundance of the dominant three groups of mugilids, namely tropical, warm-water and cool-water endemics, were related to sea surface coastal temperatures. The study suggests a strong link between temperature and the distribution and abundance of the three mullet groups within estuaries and indicates the potential of this family to act as an indicator for future climate change within these systems and adjacent coastal waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Culture and hybridization experiments on an ulva clade including the Qingdao strain blooming in the yellow sea.

    PubMed

    Hiraoka, Masanori; Ichihara, Kensuke; Zhu, Wenrong; Ma, Jiahai; Shimada, Satoshi

    2011-05-05

    In the summer of 2008, immediately prior to the Beijing Olympics, a massive green tide of the genus Ulva covered the Qingdao coast of the Yellow Sea in China. Based on molecular analyses using the nuclear encoded rDNA internal transcribed spacer (ITS) region, the Qingdao strains dominating the green tide were reported to be included in a single phylogenetic clade, currently regarded as a single species. On the other hand, our detailed phylogenetic analyses of the clade, using a higher resolution DNA marker, suggested that two genetically separate entities could be included within the clade. However, speciation within the Ulva clade has not yet been examined. We examined the occurrence of an intricate speciation within the clade, including the Qingdao strains, via combined studies of culture, hybridization and phylogenetic analysis. The two entities separated by our phylogenetic analyses of the clade were simply distinguished as U. linza and U. prolifera morphologically by the absence or presence of branches in cultured thalli. The inclusion of sexual strains and several asexual strains were found in each taxon. Hybridizations among the sexual strains also supported the separation by a partial gamete incompatibility. The sexually reproducing Qingdao strains crossed with U. prolifera without any reproductive boundary, but a complete reproductive isolation to U. linza occurred by gamete incompatibility. The results demonstrate that the U. prolifera group includes two types of sexual strains distinguishable by crossing affinity to U. linza. Species identification within the Ulva clade requires high resolution DNA markers and/or hybridization experiments and is not possible by reliance on the ITS markers alone.

  3. Are coastal protected areas always effective in achieving population recovery for nesting sea turtles?

    PubMed

    Nel, Ronel; Punt, André E; Hughes, George R

    2013-01-01

    Sea turtles are highly migratory and usually dispersed, but aggregate off beaches during the nesting season, rendering them vulnerable to coastal threats. Consequently, coastal Marine Protection Areas (MPAs) have been used to facilitate the recovery of turtle populations, but the effectiveness of these programs is uncertain as most have been operating for less than a single turtle generation (or<20 yr). South Africa, however, hosts one of the longest running conservation programs, protecting nesting loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) turtles since 1963 in a series of coastal MPAs. This provides a unique opportunity to evaluate the long-term effect of spatial protection on the abundance of two highly migratory turtle species with different life history characteristics. Population responses were assessed by modeling the number of nests over time in an index area (13 km) and an expanded monitoring area (53 km) with varying survey effort. Loggerhead abundance increased dramatically from∼250 to>1700 nests pa (index area) especially over the last decade, while leatherback abundance increased initially∼10 to 70 nests pa (index area), but then stabilized. Although leatherbacks have higher reproductive output per female and comparable remigration periods and hatching success to loggerheads, the leatherback population failed to expand. Our results suggest that coastal MPAs can work but do not guarantee the recovery of sea turtle populations as pressures change over time. Causes considered for the lack of population growth include factors in the MPA (expansion into unmonitored areas or incubation environment) of outside of the MPA (including carrying capacity and fishing mortality). Conservation areas for migratory species thus require careful design to account for species-specific needs, and need to be monitored to keep track of changing pressures.

  4. Are Coastal Protected Areas Always Effective in Achieving Population Recovery for Nesting Sea Turtles?

    PubMed Central

    Nel, Ronel; Punt, André E.; Hughes, George R.

    2013-01-01

    Sea turtles are highly migratory and usually dispersed, but aggregate off beaches during the nesting season, rendering them vulnerable to coastal threats. Consequently, coastal Marine Protection Areas (MPAs) have been used to facilitate the recovery of turtle populations, but the effectiveness of these programs is uncertain as most have been operating for less than a single turtle generation (or<20 yr). South Africa, however, hosts one of the longest running conservation programs, protecting nesting loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) turtles since 1963 in a series of coastal MPAs. This provides a unique opportunity to evaluate the long-term effect of spatial protection on the abundance of two highly migratory turtle species with different life history characteristics. Population responses were assessed by modeling the number of nests over time in an index area (13 km) and an expanded monitoring area (53 km) with varying survey effort. Loggerhead abundance increased dramatically from∼250 to>1700 nests pa (index area) especially over the last decade, while leatherback abundance increased initially∼10 to 70 nests pa (index area), but then stabilized. Although leatherbacks have higher reproductive output per female and comparable remigration periods and hatching success to loggerheads, the leatherback population failed to expand. Our results suggest that coastal MPAs can work but do not guarantee the recovery of sea turtle populations as pressures change over time. Causes considered for the lack of population growth include factors in the MPA (expansion into unmonitored areas or incubation environment) of outside of the MPA (including carrying capacity and fishing mortality). Conservation areas for migratory species thus require careful design to account for species-specific needs, and need to be monitored to keep track of changing pressures. PMID:23671683

  5. Metal discharges by Sinaloa Rivers to the coastal zone of NW Mexico.

    PubMed

    Frías-Espericueta, M G; Mejía-Cruz, R; Osuna López, I; Muy-Rangel, M D; Rubio-Carrasco, W; Aguilar-Juárez, M; Voltolina, D

    2014-02-01

    The aim of this work was to survey the discharges of dissolved and particulate Cd, Cu, Fe, Mn, Pb and Zn of the eight main rivers of Sinaloa State to the Mexican coastal environment. Zn was the most abundant dissolved metal and Fe was the most abundant particulate (8.02-16.90 and 51.8-1,140.3 μg/L, respectively). Only particulate Mn had significantly (p = 0.028) higher values in summer-fall (rainy season), whereas the significantly (p = 0.036) higher values of dissolved Zn were observed in winter and spring. The highest annual total discharges to Sinaloa coastal waters were those of the rivers San Lorenzo and Piaxtla (>2 × 10(3) m.t.) and the lowest those of rivers Baluarte and El Fuerte (349 and 119 m.t., respectively). Pb concentrations may become of concern, because they are higher than the value recommended for the welfare of aquatic communities of natural waters.

  6. Mercury dynamics in a coastal plain watershed: insights from multiple models and empirical data

    EPA Science Inventory

    Interactions among atmospherically deposited mercury, abundant wetlands, and surface waters with elevated acidity and dissolved organic carbon (DOC) often lead to widespread mercury-related fish consumption advisories in the Coastal Plain of the southeastern United States (US). H...

  7. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss

    PubMed Central

    Braukmann, Thomas

    2013-01-01

    The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades ‘O’ and ‘K’) exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the ‘O’ clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The ‘K’ clade also exhibits considerable loss of plastid genes. Unlike in the ‘O’ clade, in which all species seem to be affected, the losses in clade ‘K’ progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites ‘in action’. The widespread plastid gene loss in these two clades is

  8. BIVALVE BIOGEOGRAPHIC DISTRIBUTIONS, ABUNDANCES, AND CLIMATE VULNERABILITY FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

    EPA Science Inventory

    As part of an U.S. EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change along the Pacific Coast, we have synthesized the biogeographic distributions and abundances of bivalves found in depths <200 m. We have included the twelve &ldqu...

  9. Genetic identification and evolutionary trends of the seagrass Halophila nipponica in temperate coastal waters of Korea.

    PubMed

    Kim, Young Kyun; Kim, Seung Hyeon; Yi, Joo Mi; Kang, Chang-Keun; Short, Frederick; Lee, Kun-Seop

    2017-01-01

    Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past. We used a phylogenetic analysis of internal transcribed spacer (ITS) regions to examine the genetic variability and evolutionary trend of H. nipponica. ITS sequences of H. nipponica from various locations in Korea and Japan were identical or showed very low sequence divergence (less than 3-base pair, bp, difference), confirming that H. nipponica from Japan and Korea are the same species. Halophila species in the section Halophila, which have simple phyllotaxy (a pair of petiolate leaves at the rhizome node), were separated into five well-supported clades by maximum parsimony analysis. H. nipponica grouped with H. okinawensis and H. gaudichaudii from the subtropical regions in the same clade, the latter two species having quite low ITS sequence divergence from H. nipponica (7-15-bp). H. nipponica in Clade I diverged 2.95 ± 1.08 million years ago from species in Clade II, which includes H. ovalis. According to geographical distribution and genetic similarity, H. nipponica appears to have diverged from a tropical species like H. ovalis and adapted to warm temperate environments. The results of divergence time estimates suggest that the temperate H. nipponica is an older species than the subtropical H. okinawensis and H. gaudichaudii and they may have different evolutionary histories.

  10. Genetic identification and evolutionary trends of the seagrass Halophila nipponica in temperate coastal waters of Korea

    PubMed Central

    Kim, Young Kyun; Kim, Seung Hyeon; Yi, Joo Mi; Kang, Chang-Keun; Short, Frederick; Lee, Kun-Seop

    2017-01-01

    Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past. We used a phylogenetic analysis of internal transcribed spacer (ITS) regions to examine the genetic variability and evolutionary trend of H. nipponica. ITS sequences of H. nipponica from various locations in Korea and Japan were identical or showed very low sequence divergence (less than 3-base pair, bp, difference), confirming that H. nipponica from Japan and Korea are the same species. Halophila species in the section Halophila, which have simple phyllotaxy (a pair of petiolate leaves at the rhizome node), were separated into five well-supported clades by maximum parsimony analysis. H. nipponica grouped with H. okinawensis and H. gaudichaudii from the subtropical regions in the same clade, the latter two species having quite low ITS sequence divergence from H. nipponica (7–15-bp). H. nipponica in Clade I diverged 2.95 ± 1.08 million years ago from species in Clade II, which includes H. ovalis. According to geographical distribution and genetic similarity, H. nipponica appears to have diverged from a tropical species like H. ovalis and adapted to warm temperate environments. The results of divergence time estimates suggest that the temperate H. nipponica is an older species than the subtropical H. okinawensis and H. gaudichaudii and they may have different evolutionary histories. PMID:28505209

  11. Juvenile skeletogenesis in anciently diverged sea urchin clades.

    PubMed

    Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

    2015-04-01

    Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in

  12. Monitoring Bloom Dynamics of a Common Coastal Bioluminescent Ctenophore

    DTIC Science & Technology

    2008-01-01

    profound impacts on coastal ecosystems. Although the causes of jellyfish blooms are not well understood, correlations have been made between...changes in jellyfish density and changes in physical factors, such as temperature and salinity, and biological factors, such as prey abundance and...Current sampling methods for jellyfish populations are done with net collections by hand at stations weekly, monthly, or seasonally. These time scales

  13. Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

    USDA-ARS?s Scientific Manuscript database

    Previous phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains...

  14. Repeated count surveys help standardize multi-agency estimates of American Oystercatcher (Haematopus palliatus) abundance

    USGS Publications Warehouse

    Hostetter, Nathan J.; Gardner, Beth; Schweitzer, Sara H.; Boettcher, Ruth; Wilke, Alexandra L.; Addison, Lindsay; Swilling, William R.; Pollock, Kenneth H.; Simons, Theodore R.

    2015-01-01

    The extensive breeding range of many shorebird species can make integration of survey data problematic at regional spatial scales. We evaluated the effectiveness of standardized repeated count surveys coordinated across 8 agencies to estimate the abundance of American Oystercatcher (Haematopus palliatus) breeding pairs in the southeastern United States. Breeding season surveys were conducted across coastal North Carolina (90 plots) and the Eastern Shore of Virginia (3 plots). Plots were visited on 1–5 occasions during April–June 2013. N-mixture models were used to estimate abundance and detection probability in relation to survey date, tide stage, plot size, and plot location (coastal bay vs. barrier island). The estimated abundance of oystercatchers in the surveyed area was 1,048 individuals (95% credible interval: 851–1,408) and 470 pairs (384–637), substantially higher than estimates that did not account for detection probability (maximum counts of 674 individuals and 316 pairs). Detection probability was influenced by a quadratic function of survey date, and increased from mid-April (~0.60) to mid-May (~0.80), then remained relatively constant through June. Detection probability was also higher during high tide than during low, rising, or falling tides. Abundance estimates from N-mixture models were validated at 13 plots by exhaustive productivity studies (2–5 surveys wk−1). Intensive productivity studies identified 78 breeding pairs across 13 productivity plots while the N-mixture model abundance estimate was 74 pairs (62–119) using only 1–5 replicated surveys season−1. Our results indicate that standardized replicated count surveys coordinated across multiple agencies and conducted during a relatively short time window (closure assumption) provide tremendous potential to meet both agency-level (e.g., state) and regional-level (e.g., flyway) objectives in large-scale shorebird monitoring programs.

  15. The spread of highly pathogenic avian influenza (subtype H5N1) clades in Bangladesh, 2010 and 2011.

    PubMed

    Osmani, Muzaffar G; Ward, Michael P; Giasuddin, Md; Islam, Md Rafiqul; Kalam, Abul

    2014-04-01

    Since the global spread of highly pathogenic avian influenza H5N1 during 2005-2006, control programs have been successfully implemented in most affected countries. HPAI H5N1 was first reported in Bangladesh in 2007, and since then 546 outbreaks have been reported to the OIE. The disease has apparently become endemic in Bangladesh. Spatio-temporal information on 177 outbreaks of HPAI H5N1 occurring between February 2010 and April 2011 in Bangladesh, and 37 of these outbreaks in which isolated H5N1 viruses were phylogenetically characterized to clade, were analyzed. Three clades were identified, 2.2 (21 cases), 2.3.4 (2 cases) and 2.3.2.1 (14 cases). Clade 2.2 was identified throughout the time period and was widely distributed in a southeast-northwest orientation. Clade 2.3.2.1 appeared later and was generally confined to central Bangladesh in a north-south orientation. Based on a direction test, clade 2.2 viruses spread in a southeast-to-northwest direction, whereas clade 2.3.2.1 spread west-to-east. The magnitude of spread of clade 2.3.2.1 was greater relative to clade 2.2 (angular concentration 0.2765 versus 0.1860). In both cases, the first outbreak(s) were identified as early outliers, but in addition, early outbreaks (one each) of clade 2.2 were also identified in central Bangladesh and in northwest Bangladesh, a considerable distance apart. The spread of highly pathogenic avian influenza H5N1 in Bangladesh is characterized by reported long-distance translocation events. This poses a challenge to disease control efforts. Increased enforcement of biosecurity and stronger control of movements between affected farms and susceptible farms, and better surveillance and reporting, is needed. Although the movement of poultry and equipment appears to be a more likely explanation for the patterns identified, the relative contribution of trade and the market chain versus wild birds in spreading the disease needs further investigation. Copyright © 2014 Elsevier B.V. All

  16. Crimean-Congo Hemorrhagic Fever Virus Clade IV (Asia 1) in Ticks of Western Iran.

    PubMed

    Kayedi, Mohammad Hassan; Chinikar, Sadegh; Mostafavi, Ehsan; Khakifirouz, Sahar; Jalali, Tahmineh; Hosseini-Chegeni, Asadolah; Naghizadeh, Ali; Niedrig, Matthias; Fooks, Anthony R; Shahhosseini, Nariman

    2015-09-01

    Crimean-Congo Hemorrhagic Fever virus (CCHFV) is transmitted through the bite of an infected tick, or by direct contact with CCHFV-infected patients' blood or the products of infected livestock. In 2012, ticks were collected in eight regions of Lorestan Province, Iran. In total, 434 ticks were collected. Reverse transcriptase polymerase chain reaction was used for the detection of CCHFV RNA. Of 434 ticks, 419 (96.6%) ticks were from the family Ixodidae (hard ticks) and 15 (3.5%) ticks were from the family Argasidae (soft ticks). The presence of CCHFV RNA was detected in 29 (6.7%) of 434 ticks. The infected tick species include Hyalomma asiaticum (n = 7, 7.4%), Hyalomma anatolicum (n = 12, 13.2%), Hyalomma marginatum (n = 1, 16.7%), and Rhipicephalus sanguineus (n = 9, 4.3%). These empirical data demonstrated that the majority of CCHFV-positive ticks belonged to the Ixodidae. None of the Argasidae and Haemaphysalis sulcata species was infected with CCHFV. The phylogenetic analyses of the tick-derived CCHFV strains revealed that all 29 viral strains fell in clade IV (Asia 1). The most abundant species of tick collected in this study was R. sanguineus followed by different species of Hyalomma. Given the infection rate among collected ticks, H. marginatum was the most abundant infected tick species (16.7%) followed by H. anatolicum (13.2%), H. asiaticum (7.4%), and R. sanguineus (4.3%). © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

    PubMed Central

    Blanga-Kanfi, Shani; Miranda, Hector; Penn, Osnat; Pupko, Tal; DeBry, Ronald W; Huchon, Dorothée

    2009-01-01

    Background Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. Conclusion Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset. PMID:19341461

  18. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences.

    PubMed

    Söllinger, Andrea; Schwab, Clarissa; Weinmaier, Thomas; Loy, Alexander; Tveit, Alexander T; Schleper, Christa; Urich, Tim

    2016-01-01

    Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Cross-reactivity of anti-HIV-1 T cell immune responses among the major HIV-1 clades in HIV-1-positive individuals from 4 continents.

    PubMed

    Coplan, Paul M; Gupta, Swati B; Dubey, Sheri A; Pitisuttithum, Punnee; Nikas, Alex; Mbewe, Bernard; Vardas, Efthyia; Schechter, Mauro; Kallas, Esper G; Freed, Dan C; Fu, Tong-Ming; Mast, Christopher T; Puthavathana, Pilaipan; Kublin, James; Brown Collins, Kelly; Chisi, John; Pendame, Richard; Thaler, Scott J; Gray, Glenda; Mcintyre, James; Straus, Walter L; Condra, Jon H; Mehrotra, Devan V; Guess, Harry A; Emini, Emilio A; Shiver, John W

    2005-05-01

    The genetic diversity of human immunodeficiency virus type 1 (HIV-1) raises the question of whether vaccines that include a component to elicit antiviral T cell immunity based on a single viral genetic clade could provide cellular immune protection against divergent HIV-1 clades. Therefore, we quantified the cross-clade reactivity, among unvaccinated individuals, of anti-HIV-1 T cell responses to the infecting HIV-1 clade relative to other major circulating clades. Cellular immune responses to HIV-1 clades A, B, and C were compared by standardized interferon- gamma enzyme-linked immunospot assays among 250 unvaccinated individuals, infected with diverse HIV-1 clades, from Brazil, Malawi, South Africa, Thailand, and the United States. Cross-clade reactivity was evaluated by use of the ratio of responses to heterologous versus homologous (infecting) clades of HIV-1. Cellular immune responses were predominantly focused on viral Gag and Nef proteins. Cross-clade reactivity of cellular immune responses to HIV-1 clade A, B, and C proteins was substantial for Nef proteins (ratio, 0.97 [95% confidence interval, 0.89-1.05]) and lower for Gag proteins (ratio, 0.67 [95% confidence interval, 0.62-0.73]). The difference in cross-clade reactivity to Nef and Gag proteins was significant (P<.0001). Cross-clade reactivity of cellular immune responses can be substantial but varies by viral protein.

  20. Decoupled form and function in disparate herbivorous dinosaur clades

    NASA Astrophysics Data System (ADS)

    Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

    2016-05-01

    Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

  1. Decoupled form and function in disparate herbivorous dinosaur clades.

    PubMed

    Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

    2016-05-20

    Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

  2. Coastal system mapping: a new approach to formalising and conceptualising the connectivity of large-scale coastal systems

    NASA Astrophysics Data System (ADS)

    French, J.; Burningham, H.; Whitehouse, R.

    2010-12-01

    pertaining to specific locations to be embedded in system maps. Exported maps can be analysed separately to quantify abundance of system components and their scales of interaction. Our approach is demonstrated for different scales and geomorphic contexts in the UK, including Alnmouth Bay (NE England; 15km), Lowestoft to Felixstowe (E England; 73km) and Cardigan Bay (Wales; 267km). Aerial imagery provides the primary basis for identifying features and elements and likely modes of interaction. This interpretation is then checked against relevant research literature and site data. Coastal system mapping is a kind of knowledge formalisation that generalises disparate sources of information (‘plain data’) into usable knowledge. Consensus-derived system maps are highly effective as a catalyst for structured discussion of geomorphic system behaviour and its implications for coastal management. They also function as a repository for results from quantitative analyses and modelling.

  3. Major clades of Agaricales: a multilocus phylogenetic overview.

    Treesearch

    P. Brandon Matheny; Judd M. Curtis; Valerie Hofstetter; M. Catherine Aime; Jean-Marc Moncalvo; Zai-Wei Ge; Zhu-Liang Yang; Joseph F. Ammirati; Timothy J. Baroni; Neale L. Bougher; Karen W. Lodge Hughes; Richard W. Kerrigan; Michelle T. Seidl; Aanen; Matthew Duur K. DeNitis; Graciela M. Daniele; Dennis E. Desjardin; Bradley R. Kropp; Lorelei L. Norvell; Andrew Parker; Else C. Vellinga; Rytas Vilgalys; David S. Hibbett

    2006-01-01

    An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid,...

  4. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal

    PubMed Central

    Guimarães, Monick L.; Morgado, Mariza G.; Bello, Gonzalo

    2015-01-01

    The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades. PMID:25993094

  5. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal.

    PubMed

    de Pina-Araujo, Isabel Inês M; Delatorre, Edson; Guimarães, Monick L; Morgado, Mariza G; Bello, Gonzalo

    2015-01-01

    The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called G(CV-PT)). The G(CV-PT) clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the G(CV-PT) clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the G(CV-PT) clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the G(CV-PT )and CRF14_BG clades.

  6. Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China

    PubMed Central

    Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin

    2016-01-01

    ABSTRACT The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 106 50% egg infective doses (EID50). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. IMPORTANCE Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of

  7. Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China.

    PubMed

    Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin; Chen, Hualan

    2016-11-01

    The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 10 6 50% egg infective doses (EID 50 ). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of poultry. Here, we

  8. Spatially uniform but temporally variable bacterioplankton in a semi-enclosed coastal area.

    PubMed

    Meziti, Alexandra; Kormas, Konstantinos A; Moustaka-Gouni, Maria; Karayanni, Hera

    2015-07-01

    Studies focusing on the temporal and spatial dynamics of bacterioplankton communities within littoral areas undergoing direct influences from the coast are quite limited. In addition, they are more complicated to resolve compared to communities in the open ocean. In order to elucidate the effects of spatial vs. temporal variability on bacterial communities in a highly land-influenced semi-enclosed gulf, surface bacterioplankton communities from five coastal sites in Igoumenitsa Gulf (Ionian Sea, Greece) were analyzed over a nine-month period using 16S rDNA 454-pyrosequencing. Temporal differences were more pronounced than spatial ones, with lower diversity indices observed during the summer months. During winter and early spring, bacterial communities were dominated by SAR11 representatives, while this pattern changed in May when they were abruptly replaced by members of Flavobacteriales, Pseudomonadales, and Alteromonadales. Additionally, correlation analysis showed high negative correlations between the presence of SAR11 OTUs in relation to temperature and sunlight that might have driven, directly or indirectly, the disappearance of these OTUs in the summer months. The dominance of SAR11 during the winter months further supported the global distribution of the clade, not only in the open-sea, but also in coastal systems. This study revealed that specific bacteria exhibited distinct succession patterns in an anthropogenic-impacted coastal system. The major bacterioplankton component was represented by commonly found marine bacteria exhibiting seasonal dynamics, while freshwater and terrestrial-related phylotypes were absent. Copyright © 2015 Elsevier GmbH. All rights reserved.

  9. Distribution, abundance, diversity and habitat associations of fishes across a bioregion experiencing rapid coastal development

    NASA Astrophysics Data System (ADS)

    McLean, Dianne L.; Langlois, Tim J.; Newman, Stephen J.; Holmes, Thomas H.; Birt, Matthew J.; Bornt, Katrina R.; Bond, Todd; Collins, Danielle L.; Evans, Scott N.; Travers, Michael J.; Wakefield, Corey B.; Babcock, Russ C.; Fisher, Rebecca

    2016-09-01

    Knowledge of the factors that influence spatial patterns in fish abundance, distribution and diversity are essential for informing fisheries and conservation management. The present study was conducted in the nearshore Pilbara bioregion of north-western Australia where the dynamic marine environment is characterised by large embayments, numerous islands and islets, coexisting with globally significant petrochemical and mineral industries. Within Western Australia, this nearshore bioregion has high biodiversity and is considered to play an essential role in the recruitment of species of commercial importance. To better inform future investigations into both ecological processes and planning scenarios for management, a rapid assessment of the distribution, abundance and associations with nearshore habitats of fishes across the region was conducted. Baited remote underwater stereo-video systems (stereo-BRUVs) were used to simultaneously sample the fish assemblage and habitat composition. Generalised additive mixed models (GAMMs) were used to determine whether the abundance of fishes were related to habitat and a range of environmental variables (visibility, depth, distance to 30 m and 200 m depth isobars, boat ramps and the nearest large embayment (Exmouth Gulf). A diverse fish assemblage comprising 343 species from 58 families was recorded. The abundance and distribution patterns of fishery-target species and of the five most common and abundant species and families were linked positively with areas of high relief, hard coral cover, reef and macroalgae and negatively with the distance to the nearest oceanic waters (200 m depth isobar). This study provides information that can contribute to future marine spatial planning scenarios for management of the Pilbara using a unique, analytical approach that has broad application in biogeography.

  10. Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

    PubMed

    Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

    2014-12-01

    Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments.

  11. Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

    PubMed

    Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

    2014-11-11

    Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments.

  12. Short Report: Comparison of Oral Infectious Dose of West Nile Virus Isolates Representing Three Distinct Genotypes in Culex quinquefasciatus

    PubMed Central

    Vanlandingham, Dana L.; McGee, Charles E.; Klingler, Kimberly A.; Galbraith, Sareen E.; Barrett, Alan D. T.; Higgs, Stephen

    2009-01-01

    Phylogenetic analysis of West Nile virus in North America has identified replacement of the originally introduced clade, Eastern United States (NY99), by the North American clade. In addition, the transient emergence of other clades and genetic variants has also been observed. In this study, we investigated the potential role of the mosquito in the selection of these clades and genetic variants. We determined the relative susceptibility of Culex quinquefasciatus to infection with isolates from the Eastern U.S. clade, the North American clade, and the Southeast coastal Texas clade. Although significant differences were observed in 50% oral infectious dose values between the Eastern U.S. and two attenuated North American genetic variants compared with the North American and Southeast coastal Texas clade viruses, these differences did not correlate with persistence of the genotype in nature. These results indicate that selection of these viral genotypes was independent of viral oral infectivity in the mosquito. PMID:19052310

  13. Abundance and Diversity of Crypto- and Necto-Benthic Coastal Fish Are Higher in Marine Forests than in Structurally Less Complex Macroalgal Assemblages

    PubMed Central

    Thiriet, Pierre D.; Cheminée, Adrien; Guidetti, Paolo; Bianchimani, Olivier; Basthard-Bogain, Solène; Cottalorda, Jean-Michel; Arceo, Hazel; Moranta, Joan; Lejeune, Pierre; Francour, Patrice; Mangialajo, Luisa

    2016-01-01

    In Mediterranean subtidal rocky reefs, Cystoseira spp. (Phaeophyceae) form dense canopies up to 1 m high. Such habitats, called ‘Cystoseira forests’, are regressing across the entire Mediterranean Sea due to multiple anthropogenic stressors, as are other large brown algae forests worldwide. Cystoseira forests are being replaced by structurally less complex habitats, but little information is available regarding the potential difference in the structure and composition of fish assemblages between these habitats. To fill this void, we compared necto-benthic (NB) and crypto-benthic (CB) fish assemblage structures between Cystoseira forests and two habitats usually replacing the forests (turf and barren), in two sampling regions (Corsica and Menorca). We sampled NB fish using Underwater Visual Census (UVC) and CB fish using Enclosed Anaesthetic Station Vacuuming (EASV), since UVC is known to underestimate the diversity and density of the ‘hard to spot’ CB fish. We found that both taxonomic diversity and total density of NB and CB fish were highest in Cystoseira forests and lowest in barrens, while turfs, that could be sampled only at Menorca, showed intermediate values. Conversely, total biomass of NB and CB fish did not differ between habitats because the larger average size of fish in barrens (and turfs) compensated for their lower densities. The NB families Labridae and Serranidae, and the CB families Blenniidae, Cliniidae, Gobiidae, Trypterigiidae and Scorpaenidae, were more abundant in forests. The NB taxa Diplodus spp. and Thalassoma pavo were more abundant in barrens. Our study highlights the importance of using EASV for sampling CB fish, and shows that Cystoseira forests support rich and diversified fish assemblages. This evidence suggests that the ongoing loss of Cystoseira forests may impair coastal fish assemblages and related goods and services to humans, and stresses the need to implement strategies for the successful conservation and/or recovery

  14. Abundance and Diversity of Crypto- and Necto-Benthic Coastal Fish Are Higher in Marine Forests than in Structurally Less Complex Macroalgal Assemblages.

    PubMed

    Thiriet, Pierre D; Di Franco, Antonio; Cheminée, Adrien; Guidetti, Paolo; Bianchimani, Olivier; Basthard-Bogain, Solène; Cottalorda, Jean-Michel; Arceo, Hazel; Moranta, Joan; Lejeune, Pierre; Francour, Patrice; Mangialajo, Luisa

    2016-01-01

    In Mediterranean subtidal rocky reefs, Cystoseira spp. (Phaeophyceae) form dense canopies up to 1 m high. Such habitats, called 'Cystoseira forests', are regressing across the entire Mediterranean Sea due to multiple anthropogenic stressors, as are other large brown algae forests worldwide. Cystoseira forests are being replaced by structurally less complex habitats, but little information is available regarding the potential difference in the structure and composition of fish assemblages between these habitats. To fill this void, we compared necto-benthic (NB) and crypto-benthic (CB) fish assemblage structures between Cystoseira forests and two habitats usually replacing the forests (turf and barren), in two sampling regions (Corsica and Menorca). We sampled NB fish using Underwater Visual Census (UVC) and CB fish using Enclosed Anaesthetic Station Vacuuming (EASV), since UVC is known to underestimate the diversity and density of the 'hard to spot' CB fish. We found that both taxonomic diversity and total density of NB and CB fish were highest in Cystoseira forests and lowest in barrens, while turfs, that could be sampled only at Menorca, showed intermediate values. Conversely, total biomass of NB and CB fish did not differ between habitats because the larger average size of fish in barrens (and turfs) compensated for their lower densities. The NB families Labridae and Serranidae, and the CB families Blenniidae, Cliniidae, Gobiidae, Trypterigiidae and Scorpaenidae, were more abundant in forests. The NB taxa Diplodus spp. and Thalassoma pavo were more abundant in barrens. Our study highlights the importance of using EASV for sampling CB fish, and shows that Cystoseira forests support rich and diversified fish assemblages. This evidence suggests that the ongoing loss of Cystoseira forests may impair coastal fish assemblages and related goods and services to humans, and stresses the need to implement strategies for the successful conservation and/or recovery of marine

  15. The invasive ant, Solenopsis invicta, reduces herpetofauna richness and abundance

    USGS Publications Warehouse

    Allen, Craig R.; Birge, Hannah E.; Slater, J.; Wiggers, E.

    2017-01-01

    Amphibians and reptiles are declining globally. One potential cause of this decline includes impacts resulting from co-occurrence with non-native red imported fire ant, Solenopsis invicta. Although a growing body of anecdotal and observational evidence from laboratory experiments supports this hypothesis, there remains a lack of field scale manipulations testing the effect of fire ants on reptile and amphibian communities. We addressed this gap by measuring reptile and amphibian (“herpetofauna”) community response to successful fire ant reductions over the course of 2 years following hydramethylnon application to five 100–200 ha plots in southeastern coastal South Carolina. By assessing changes in relative abundance and species richness of herpetofauna in response to fire ant reductions, we were able to assess whether some species were particularly vulnerable to fire ant presence, and whether this sensitivity manifested at the community level. We found that herpetofauna abundance and species richness responded positively to fire ant reductions. Our results document that even moderate populations of red imported fire ants decrease both the abundance and diversity of herpetofauna. Given global herpetofauna population declines and continued spread of fire ants, there is urgency to understand the impacts of fire ants beyond anecdotal and singles species studies. Our results provides the first community level investigation addressing these dynamics, by manipulating fire ant abundance to reveal a response in herpetofauna species abundance and richness.

  16. Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.

    PubMed

    Christensen, Geoff A; Wymore, Ann M; King, Andrew J; Podar, Mircea; Hurt, Richard A; Santillan, Eugenio U; Soren, Ally; Brandt, Craig C; Brown, Steven D; Palumbo, Anthony V; Wall, Judy D; Gilmour, Cynthia C; Elias, Dwayne A

    2016-10-01

    Two genes, hgcA and hgcB, are essential for microbial mercury (Hg) methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability, and biogeochemistry, are critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea genomes. A distinct PCR product at the expected size was confirmed for all hgcAB(+) strains tested via Sanger sequencing. Additionally, we developed clade-specific degenerate quantitative PCR (qPCR) primers that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88%, and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes, and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. The resulting data will be essential in developing accurate and robust predictive models of Hg methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB IMPORTANCE: The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microorganisms. The recent

  17. Normal and Extreme Wind Conditions for Power at Coastal Locations in China.

    PubMed

    Gao, Meng; Ning, Jicai; Wu, Xiaoqing

    2015-01-01

    In this paper, the normal and extreme wind conditions for power at 12 coastal locations along China's coastline were investigated. For this purpose, the daily meteorological data measured at the standard 10-m height above ground for periods of 40-62 years are statistically analyzed. The East Asian Monsoon that affects almost China's entire coastal region is considered as the leading factor determining wind energy resources. For most stations, the mean wind speed is higher in winter and lower in summer. Meanwhile, the wind direction analysis indicates that the prevalent winds in summer are southerly, while those in winter are northerly. The air densities at different coastal locations differ significantly, resulting in the difference in wind power density. The Weibull and lognormal distributions are applied to fit the yearly wind speeds. The lognormal distribution performs better than the Weibull distribution at 8 coastal stations according to two judgement criteria, the Kolmogorov-Smirnov test and absolute error (AE). Regarding the annual maximum extreme wind speed, the generalized extreme value (GEV) distribution performs better than the commonly-used Gumbel distribution. At these southeastern coastal locations, strong winds usually occur in typhoon season. These 4 coastal provinces, that is, Guangdong, Fujian, Hainan, and Zhejiang, which have abundant wind resources, are also prone to typhoon disasters.

  18. [Comparative foliar anatomy and systematics of the Trichocentrum-clade with emphasis in Cohniella (Asparagales: Orchidaceae)].

    PubMed

    Cetzal-Ix, William; Noguera-Savelli, Eliana; Jáuregui, Damelis; Carnevali, Germáin

    2013-12-01

    The genera Cohniella, Lophiarella, Lophiaris, and Trichocentrum are included in the Trichocentrum-clade. These genera are distributed from Florida and Northern Mexico to Southern Brazil and Northern Argentina, growing in tropical deciduous forests or tropical rain forests and thorn scrub forests to pine-oak forest, from sea level to 1700 m. The leaf anatomical structure of 23 members of the Trichocentrum-clade was explored as a source of taxonomic and phylogenetic characters. A total of 11 species of Cohniella, three species of Lophiarella, seven species of Lophiaris, two species of Trichocentrum, and other four species were included as outgroup. Anatomical characters were studied by cross sections and paradermic observations of the middle portion of fresh leaves. Although anatomical characters were fairly homogeneous throughout the clade, twelve vegetative anatomical, phylogenetically informative characters were selected and coded for an analysis that was performed using an exhaustive search (implicit enumeration) implemented through TNT. The strict consensus of 2692 most parsimonious trees resulted in a poorly resolved polytomy, which however recovers the Trichocentrum-clade with a monophyletic, strongly supported Cohniella nested within it with unifacial leaves and the presence of cellular inclusions in the epidermis as synapomorphies. We concluded that the anatomy characters alone are insufficient to assess the relationships amongst the genera of the Trichocentrum-clade. However, the two synapomorphies recovered for Cohniella strongly support its monophyly when these are analyzed in conjunction with other data sources (e.g., molecular and morphological characters).

  19. Coastal Geographic Structures in Coastal-Marine Environmental Management

    NASA Astrophysics Data System (ADS)

    Baklanov, P. Ya.; Ganzei, K. S.; Ermoshin, V. V.

    2018-01-01

    It has been proposed to distinguish the coastal geographic structures consisting of a spatial combination of three interconnected and mutually conditioned parts (coastal-territorial, coastal, coastal-marine), which are interlinked with each other by the cumulative effect of real-energy flows. Distinguishing specific resource features of the coastal structures, by which they play a connecting role in the complex coastalmarine management, has been considered. The main integral resource feature of the coastal structures is their connecting functions, which form transitional parts mutually connecting the coastal-territorial and coastalmarine environmental management.

  20. Phylogeny and biogeography of the most diverse clade of South American gymnophthalmid lizards (Squamata, Gymnophthalmidae, Cercosaurinae).

    PubMed

    Torres-Carvajal, Omar; Lobos, Simón E; Venegas, Pablo J; Chávez, Germán; Aguirre-Peñafiel, Vanessa; Zurita, Daniel; Echevarría, Lourdes Y

    2016-06-01

    Nearly 50% of the diversity of the speciose Neotropical lizard clade Gymnophthalmidae is nested within the subclade Cercosaurinae. The taxonomy of Cercosaurinae lizards has been historically confusing because many diagnostic characters of those clades traditionally ranked as genera do not represent true diagnostic apomorphies. Even though molecular phylogenies of several 'genera' have been presented in the last few years, some of them remain poorly sampled (e.g., Anadia, Echinosaura, Potamites, Riama). In this paper we present a more comprehensive phylogeny of Cercosaurinae lizards with emphasis on Andean taxa from Ecuador and Peru, as well as a time-calibrated phylogeny with reconstruction of ancestral areas. Our analysis includes 52% of all recognized species of Cercosaurinae (67 species) and 1914 characters including three mitochondrial and one nuclear gene. We find that Anadia, Echinosaura, Euspondylus, Potamites, Proctoporus, and Riama are not monophyletic: the Tepuian Anadia mcdiarmidi is not sister to Andean species of Anadia; Echinosaura sulcarostrum is not included in the same clade formed by other species of Echinosaura and their more recent common ancestor; Teuchocercus is nested within Echinosaura; species of Euspondylus included in this study are nested within Proctoporus; Riama laudahnae is included in Proctoporus; and Potamites is paraphyletic and split in two separate clades, one of which we name Gelanesaurus, also a new genus-group name. Within Potamites, P. ecpleopus is paraphyletic, and P. strangulatus strangulatus and P. strangulatus trachodus are recognized as two distinct species. We also identify three unnamed clades (i.e., not nested within any of the recognized 'genera') from Andean populations in Ecuador and Peru. The estimated age of the clade Cercosaurinae (∼60Ma) corresponds to the early stages of the northern Andes. Even though the distribution of the most recent common ancestor of Cercosaurinae remains equivocal, our analysis shows

  1. Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

    PubMed

    Serrano-Serrano, Martha Liliana; Perret, Mathieu; Guignard, Maïté; Chautems, Alain; Silvestro, Daniele; Salamin, Nicolas

    2015-11-10

    Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

  2. Status of the amphipod Diporeia ssp. in coastal waters of the Laurentian Great Lakes

    EPA Science Inventory

    Diporeia has historically been the dominant benthic macroinvertebrate in deeper waters of the Laurentian Great Lakes, and its abundance has been proposed as an indicator of ecological condition. In 2010, the USEPA incorporated the Great Lakes into the National Coastal Condition A...

  3. Macroclimatic change expected to transform coastal wetland ecosystems this century

    USGS Publications Warehouse

    Gabler, Christopher A.; Osland, Michael J.; Grace, James B.; Stagg, Camille L.; Day, Richard H.; Hartley, Stephen B.; Enwright, Nicholas M.; From, Andrew; McCoy, Meagan L.; McLeod, Jennie L.

    2017-01-01

    Coastal wetlands, existing at the interface between land and sea, are highly vulnerable to climate change. Macroclimate (for example, temperature and precipitation regimes) greatly influences coastal wetland ecosystem structure and function. However, research on climate change impacts in coastal wetlands has concentrated primarily on sea-level rise and largely ignored macroclimatic drivers, despite their power to transform plant community structure and modify ecosystem goods and services. Here, we model wetland plant community structure based on macroclimate using field data collected across broad temperature and precipitation gradients along the northern Gulf of Mexico coast. Our analyses quantify strongly nonlinear temperature thresholds regulating the potential for marsh-to-mangrove conversion. We also identify precipitation thresholds for dominance by various functional groups, including succulent plants and unvegetated mudflats. Macroclimate-driven shifts in foundation plant species abundance will have large effects on certain ecosystem goods and services. Based on current and projected climatic conditions, we project that transformative ecological changes are probable throughout the region this century, even under conservative climate scenarios. Coastal wetland ecosystems are functionally similar worldwide, so changes in this region are indicative of potential future changes in climatically similar regions globally.

  4. Design research about coastal zone planning and management information system based on GIS and database technologies

    NASA Astrophysics Data System (ADS)

    Huang, Pei; Wu, Sangyun; Feng, Aiping; Guo, Yacheng

    2008-10-01

    As littoral areas in possession of concentrated population, abundant resources, developed industry and active economy, the coastal areas are bound to become the forward positions and supported regions for marine exploitation. In the 21st century, the pressure that coastal zones are faced with is as follows: growth of population and urbanization, rise of sea level and coastal erosion, shortage of freshwater resource and deterioration of water resource, and degradation of fishery resource and so on. So the resources of coastal zones should be programmed and used reasonably for the sustainable development of economy and environment. This paper proposes a design research on the construction of coastal zone planning and management information system based on GIS and database technologies. According to this system, the planning results of coastal zones could be queried and displayed expediently through the system interface. It is concluded that the integrated application of GIS and database technologies provides a new modern method for the management of coastal zone resources, and makes it possible to ensure the rational development and utilization of the coastal zone resources, along with the sustainable development of economy and environment.

  5. Three New Soil-inhabiting Species of Trichoderma in the Stromaticum Clade with Test of Their Antagonism to Pathogens.

    PubMed

    Chen, Kai; Zhuang, Wen-Ying

    2017-09-01

    Trichoderma is a dominant component of the soil mycoflora. During the field investigations of northern, central, and southwestern China, three new species in the Stromaticum clade were encountered from soil, and named as T. hebeiense, T. sichuanense, and T. verticillatum. Their phylogenetic positions were determined by analyses of the combined two genes: partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit-encoding genes. Distinctions between the new species and their close relatives were discussed. Trichoderma hebeiense appeared as a separate terminal branch. The species is distinctive by its oblong conidia and aggregated pustules in culture. Trichoderma sichuanense features in concentric colony and produces numerous clean exudates on aerial mycelium in culture. Trichoderma verticillatum is characterized by its verticillium-like synanamorph and production of abundant chlamydospores. In vitro antagonism towards the new species was tested by dual culture technique.

  6. Quantifying Atlantic Menhaden in Estuarine and Coastal Waters of Long Island, New York Using Acoustic Methods

    NASA Astrophysics Data System (ADS)

    Lucca, Brandyn Mark

    Forage fish are an ecological cornerstone that trophically link primary production with pelagic predators such as piscivorous fish, marine mammals, seabirds, and humans. Atlantic menhaden (Brevoortia tyrannus) are one such forage fish species that can be found in both estuarine and coastal waters from the Gulf of Maine to Florida throughout the year. Alongside their ecological importance as prey for commercially important species such as striped bass and bluefin tuna, menhaden are fished to be used as bait or reduced into oil. New York has an especially rich history with the commercial harvesting of menhaden beginning in the late 17th century. Despite their relative ecological and economic importance, there is a paucity of quantitative data that describes the spatial and temporal distributions of menhaden in many regions throughout their geographic range. A promising method to study the distribution of menhaden is active acoustics which has been utilized in other fisheries to provide relatively time-efficient quantitative data with broad spatial coverage and high resolution. Acoustic surveys were conducted in two different habitats (estuarine, coastal) where menhaden are found during the 2014 and 2015. Menhaden aggregations were very patchy and there was evidence of significant clustering in both habitats. Coastal menhaden abundance and biomass were relatively constant throughout the summer with a peak in the late-summer. Conversely, estuarine menhaden abundance and biomass biomass peaked in late-spring and early-fall, and decreased by three orders of magnitude by mid-fall. Mean target strength (TS) of coastal menhaden was relatively constant which suggested no differences in the size classes of fish. Conversely estuarine TS distributions shifted throughout the sampling effort which were consistent with changes in the size classes of fish as they grow and migrate in and out of the estuarine habitat. This study demonstrates that active acoustics is a viable tool for

  7. Genetic diversity and temporal variation of the marine Synechococcus community in the subtropical coastal waters of Hong Kong.

    PubMed

    Jing, Hongmei; Zhang, Rui; Pointing, Stephen B; Liu, Hongbin; Qian, Peiyuan

    2009-03-01

    The phylogenetic diversity of the marine Synechococcus community in the subtropical coastal waters of Hong Kong, China, was examined through intergenic transcribed spacer clone libraries. All the sequences obtained fell within both marine cluster A (MC-A) and B (MC-B), with MC-A phylotypes dominating throughout the year. Distinct phylogenetic lineages specific to Hong Kong waters were detected from both MC-A and MC-B. The highest Synechococcus community diversity occurred in December, but the highest Synechococcus abundance occurred in August. On the other hand, both the abundance and diversity of Synechococcus showed a minimum in February. The remarkable seasonal variations of Synechococcus diversity observed were likely the result of the changes of hydrographic condition modulated by monsoons. Principal component analysis revealed that the in situ abiotic water characteristics, especially salinity and water turbidity, explained much of the variability of the marine Synechococcus population diversity in Hong Kong coastal waters. In addition, the temporal changes of Synechococcus abundance were largely driven by water temperature.

  8. Shorebird abundance and distribution on the coastal plain of the Arctic National Wildlife Refuge

    USGS Publications Warehouse

    Brown, S.; Bart, J.; Lanctot, Richard B.; Johnson, J.A.; Kendall, S.; Payer, D.; Johnson, J.

    2007-01-01

    The coastal plain of the Arctic National Wildlife Refuge hosts seven species of migratory shorebirds listed as highly imperiled or high priority by the U.S. Shorebird Conservation Plan and five species listed as Birds of Conservation Concern by the U.S. Fish and Wildlife Service. During the first comprehensive shorebird survey of the 674 000 ha "1002 Area" on the coastal plain, we recorded 14 species of breeding shorebirds at 197 rapidly surveyed plots during June 2002 and 2004. We also estimated detection ratios with a double counting technique, using data collected at 37 intensively studied plots located on the North Slope of Alaska and northern Canada. We stratified the study area by major habitat types, including wetlands, moist areas, uplands, and riparian areas, using previously classified Landsat imagery. We developed population estimates with confidence limits by species, and estimated the total number of shorebirds in the study area to be 230 000 (95% CI: 104 000-363 000), which exceeds the biological criterion for classification as both a Western Hemisphere Shorebird Reserve Network Site of International Importance (100 000 birds) and a Ramsar Wetland of International Importance (20 000 birds), even when conservatively estimated. Species richness and the density of many species were highest in wetland or riparian habitats, which are clustered along the coast. ?? The Cooper Ornithological Society 2007.

  9. High salmon density and low discharge create periodic hypoxia in coastal rivers

    Treesearch

    Christopher J. Sergeant; J. Ryan Bellmore; Casey McConnell; Jonathan W. Moore

    2017-01-01

    Dissolved oxygen (DO) is essential to the survival of almost all aquatic organisms. Here, we examine the possibility that abundant Pacific salmon (Oncorhynchus spp.) and low streamflow combine to create hypoxic events in coastal rivers. Using high-frequency DO time series from two similar watersheds in southeastern Alaska, we summarize DO regimes...

  10. Large wood debris recruitment on differing riparian landforms along a Gulf Coastal Plain (USA) stream: a comparison of large floods and average flows

    Treesearch

    Stephen W. Golladay; Juliann M. Battle; Brian J. Palik

    2007-01-01

    In southeastern Coastal Plain streams, wood debris can be very abundant and is recruited from extensive forested floodplains. Despite importance of wood debris, there have been few opportunities to examine recruitment and redistribution of wood in an undisturbed setting, particularly in the southeastern Coastal Plain. Following extensive flooding in 1994, measurements...

  11. Floristic Quality Index: An assessment tool for restoration projects and monitoring sites in coastal Louisiana

    USGS Publications Warehouse

    Cretini, K.F.; Steyer, G.D.

    2011-01-01

    The Coastwide Reference Monitoring System (CRMS) program was established to assess the effectiveness of individual coastal restoration projects and the cumulative effects of multiple projects at regional and coastwide scales. In order to make these assessments, analytical teams have been assembled for each of the primary data types sampled under the CRMS program, including vegetation, hydrology, landscape, and soils. These teams consist of scientists and support staff from the U.S. Geological Survey and other Federal agencies, the Louisiana Office of Coastal Protection and Restoration, and university academics. Each team is responsible for developing or identifying parameters, indices, or tools that can be used to assess coastal wetlands at various scales. The CRMS Vegetation Analytical Team has developed a Floristic Quality Index for coastal Louisiana to determine the quality of a wetland based on its plant species composition and abundance.

  12. Is Amazonia a 'museum' for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae).

    PubMed

    Schley, Rowan J; de la Estrella, Manuel; Pérez-Escobar, Oscar Alejandro; Bruneau, Anne; Barraclough, Timothy; Forest, Félix; Klitgård, Bente

    2018-09-01

    The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the 'cradle' or 'museum' model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade.

    PubMed

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Blom, Jochen; Alam, Intikhab; Bajic, Vladimir B; Stingl, Ulrich

    2017-07-01

    The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea: one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Compensating for geographic variation in detection probability with water depth improves abundance estimates of coastal marine megafauna.

    PubMed

    Hagihara, Rie; Jones, Rhondda E; Sobtzick, Susan; Cleguer, Christophe; Garrigue, Claire; Marsh, Helene

    2018-01-01

    The probability of an aquatic animal being available for detection is typically <1. Accounting for covariates that reduce the probability of detection is important for obtaining robust estimates of the population abundance and determining its status and trends. The dugong (Dugong dugon) is a bottom-feeding marine mammal and a seagrass community specialist. We hypothesized that the probability of a dugong being available for detection is dependent on water depth and that dugongs spend more time underwater in deep-water seagrass habitats than in shallow-water seagrass habitats. We tested this hypothesis by quantifying the depth use of 28 wild dugongs fitted with GPS satellite transmitters and time-depth recorders (TDRs) at three sites with distinct seagrass depth distributions: 1) open waters supporting extensive seagrass meadows to 40 m deep (Torres Strait, 6 dugongs, 2015); 2) a protected bay (average water depth 6.8 m) with extensive shallow seagrass beds (Moreton Bay, 13 dugongs, 2011 and 2012); and 3) a mixture of lagoon, coral and seagrass habitats to 60 m deep (New Caledonia, 9 dugongs, 2013). The fitted instruments were used to measure the times the dugongs spent in the experimentally determined detection zones under various environmental conditions. The estimated probability of detection was applied to aerial survey data previously collected at each location. In general, dugongs were least available for detection in Torres Strait, and the population estimates increased 6-7 fold using depth-specific availability correction factors compared with earlier estimates that assumed homogeneous detection probability across water depth and location. Detection probabilities were higher in Moreton Bay and New Caledonia than Torres Strait because the water transparency in these two locations was much greater than in Torres Strait and the effect of correcting for depth-specific detection probability much less. The methodology has application to visual survey of coastal

  15. Historical overfishing and the recent collapse of coastal ecosystems.

    PubMed

    Jackson, J B; Kirby, M X; Berger, W H; Bjorndal, K A; Botsford, L W; Bourque, B J; Bradbury, R H; Cooke, R; Erlandson, J; Estes, J A; Hughes, T P; Kidwell, S; Lange, C B; Lenihan, H S; Pandolfi, J M; Peterson, C H; Steneck, R S; Tegner, M J; Warner, R R

    2001-07-27

    Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.

  16. Changing patterns in coastal cutthroat trout (Oncorhynchus clarki clarki) diet and prey in a gradient of deciduous canopies

    USGS Publications Warehouse

    Romero, N.; Gresswell, R.E.; Li, J.L.

    2005-01-01

    We examined the influence of riparian vegetation patterns on coastal cutthroat trout Oncorhynchus clarki clarki diet and prey from the summer of 2001 through the spring of 2002. Benthic and drifting invertebrates, allochthonous prey, and fish diet were collected from deciduous, conifer, and mixed sections of three Oregon coastal watersheds. The nine sites were best characterized as a continuum of deciduous cover, and shrub cover and proportion of deciduous canopy were positively correlated (r = 0.74). Most sources of prey (benthic invertebrate biomass, allochthonous invertebrate inputs, aquatic and total invertebrate drift) and aquatic prey ingested by coastal cutthroat trout were greater where shrub cover was more abundant. Only aquatic drift, total invertebrate drift, and allochthonous invertebrates were positively correlated with deciduous vegetation. Compared with coniferous sites, allochthonous invertebrates under deciduous and mixed canopies were almost 30% more abundant. Stream discharge likely influenced seasonal fluxes of aquatic invertebrate biomass in the benthos and drift. Aquatic insects dominated gut contents during this study; however, terrestrial prey were most common in the diet during the summer and fall. In the Pacific northwest, systematic removal of deciduous riparian vegetation to promote conifers may have unintended consequences on food resources of coastal cutthroat trout and aquatic food web interactions. ?? 2005 NRC.

  17. Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

    NASA Astrophysics Data System (ADS)

    Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

    2005-12-01

    Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

  18. Dengue virus type 1 clade replacement in recurring homotypic outbreaks

    PubMed Central

    2013-01-01

    Background Recurring dengue outbreaks occur in cyclical pattern in most endemic countries. The recurrences of dengue virus (DENV) infection predispose the population to increased risk of contracting the severe forms of dengue. Understanding the DENV evolutionary mechanism underlying the recurring dengue outbreaks has important implications for epidemic prediction and disease control. Results We used a set of viral envelope (E) gene to reconstruct the phylogeny of DENV-1 isolated between the periods of 1987–2011 in Malaysia. Phylogenetic analysis of DENV-1 E gene revealed that genotype I virus clade replacements were associated with the cyclical pattern of major DENV-1 outbreaks in Malaysia. A total of 9 non-conservative amino acid substitutions in the DENV-1 E gene consensus were identified; 4 in domain I, 3 in domain II and 2 in domain III. Selection pressure analyses did not reveal any positively selected codon site within the full length E gene sequences (1485 nt, 495 codons). A total of 183 (mean dN/dS = 0.0413) negatively selected sites were found within the Malaysian isolates; neither positive nor negative selection was noted for the remaining 312 codons. All the viruses were cross-neutralized by the respective patient sera suggesting no strong support for immunological advantage of any of the amino acid substitutions. Conclusion DENV-1 clade replacement is associated with recurrences of major DENV-1 outbreaks in Malaysia. Our findings are consistent with those of other studies that the DENV-1 clade replacement is a stochastic event independent of positive selection. PMID:24073945

  19. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Wen, Donghui

    2015-05-01

    Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.

  20. Vegetation Types in Coastal Louisiana in 2007

    USGS Publications Warehouse

    Sasser, Charles E.; Visser, Jenneke M.; Mouton, Edmond; Linscombe, Jeb; Hartley, Steve B.

    2008-01-01

    During the summer and fall of 2007, the U.S. Geological Survey, the Louisiana State University Agricultural Center, and the Louisiana Department of Wildlife and Fisheries Fur and Refuge Division jointly completed an aerial survey to collect data on 2007 vegetation types in coastal Louisiana. The current map presents the data collected in this effort. The 2007 aerial survey was conducted by using techniques developed over the last thirty years while conducting similar vegetation surveys. Transects flown were oriented in a north-south direction and spaced 1.87 mi (3 km) apart and covered coastal marshes from the Texas State line to the Mississippi State line and from the northern extent of fresh marshes to the southern end of saline (saltwater) marshes on the beaches of the Gulf of Mexico or of coastal bays. Navigation along these transects and to each sampling site was accomplished by using Global Positioning System (GPS) technology and geographic information system (GIS) software. As the surveyors reached each sampling station, observed areas of marsh were assigned as fresh, intermediate, brackish, or saline (saltwater) types, and dominant plant species were listed and ranked according to abundance. Delineations of marsh boundaries usually followed natural levees, bayous, or other features that impede or restrict water flow.

  1. Molecular phylogeny of the Acre clade (Crassulaceae): dealing with the lack of definitions for Echeveria and Sedum.

    PubMed

    Carrillo-Reyes, Pablo; Sosa, Victoria; Mort, Mark E

    2009-10-01

    The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the "Acre clade", a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European-Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera--Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.

  2. Diversity of pollination ecology in the Schismatoglottis Calyptrata Complex Clade (Araceae).

    PubMed

    Hoe, Y C; Gibernau, M; Wong, S Y

    2018-05-01

    Field studies integrating pollination investigations with an assessment of floral scent composition and thermogenesis in tropical aroids are rather few. Thus, this study aimed to investigate the pollination biology of nine species belonging to Schismatoglottis Calyptrata Complex Clade. The flowering mechanism, visiting insect activities, reproductive system, thermogenesis and floral scent composition were examined. Anthesis for all species started at dawn and lasted 25-29 h. Colocasiomyia (Diptera, Drosophilidae) are considered the main pollinators for all the investigated species. Cycreon (Coleoptera, Hydrophilidae) are considered secondary pollinators as they are only present in seven of the nine host plants, despite the fact that they are the most effective pollen carrier, carrying up to 15 times more pollen grains than Colocasiomyia flies. However, the number of Colocasiomyia individuals was six times higher than Cycreon beetles. Chaloenus (Chrysomelidae, Galeuricinae) appeared to be an inadvertent pollinator. Atheta (Coleoptera, Staphylinidae) is considered a floral visitor in most investigated species of the Calyptrata Complex Clade in Sarawak, but a possible pollinator in S. muluensis. Chironomidae midges and pteromalid wasps are considered visitors in S. calyptrata. Thermogenesis in a biphasic pattern was observed in inflorescences of S. adducta, S. calyptrata, S. giamensis, S. pseudoniahensis and S. roh. The first peak occurred during pistillate anthesis; the second peak during staminate anthesis. Inflorescences of all investigated species of Calyptrata Complex Clade emitted four types of ester compound, with methyl ester-3-methyl-3-butenoic acid as a single major VOC (volatile organic compound). The appendix, pistillate zone, staminate zone and spathe emitted all these compounds. A mixed fly-beetle pollination system is considered an ancestral trait in the Calyptrata Complex Clade, persisting in Sarawak taxa, whereas the marked reduction of

  3. Multiple stressors, nonlinear effects and the implications of climate change impacts on marine coastal ecosystems.

    PubMed

    Hewitt, Judi E; Ellis, Joanne I; Thrush, Simon F

    2016-08-01

    Global climate change will undoubtedly be a pressure on coastal marine ecosystems, affecting not only species distributions and physiology but also ecosystem functioning. In the coastal zone, the environmental variables that may drive ecological responses to climate change include temperature, wave energy, upwelling events and freshwater inputs, and all act and interact at a variety of spatial and temporal scales. To date, we have a poor understanding of how climate-related environmental changes may affect coastal marine ecosystems or which environmental variables are likely to produce priority effects. Here we use time series data (17 years) of coastal benthic macrofauna to investigate responses to a range of climate-influenced variables including sea-surface temperature, southern oscillation indices (SOI, Z4), wind-wave exposure, freshwater inputs and rainfall. We investigate responses from the abundances of individual species to abundances of functional traits and test whether species that are near the edge of their tolerance to another stressor (in this case sedimentation) may exhibit stronger responses. The responses we observed were all nonlinear and some exhibited thresholds. While temperature was most frequently an important predictor, wave exposure and ENSO-related variables were also frequently important and most ecological variables responded to interactions between environmental variables. There were also indications that species sensitive to another stressor responded more strongly to weaker climate-related environmental change at the stressed site than the unstressed site. The observed interactions between climate variables, effects on key species or functional traits, and synergistic effects of additional anthropogenic stressors have important implications for understanding and predicting the ecological consequences of climate change to coastal ecosystems. © 2015 John Wiley & Sons Ltd.

  4. A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)

    Treesearch

    Beatriz Ortiz-Santana; Daniel L. Lindner; Otto Miettinen; Alfredo Justo; David S. Hibbett

    2013-01-01

    Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were...

  5. The estimation of tree posterior probabilities using conditional clade probability distributions.

    PubMed

    Larget, Bret

    2013-07-01

    In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample.

  6. Normal and Extreme Wind Conditions for Power at Coastal Locations in China

    PubMed Central

    Gao, Meng; Ning, Jicai; Wu, Xiaoqing

    2015-01-01

    In this paper, the normal and extreme wind conditions for power at 12 coastal locations along China’s coastline were investigated. For this purpose, the daily meteorological data measured at the standard 10-m height above ground for periods of 40–62 years are statistically analyzed. The East Asian Monsoon that affects almost China’s entire coastal region is considered as the leading factor determining wind energy resources. For most stations, the mean wind speed is higher in winter and lower in summer. Meanwhile, the wind direction analysis indicates that the prevalent winds in summer are southerly, while those in winter are northerly. The air densities at different coastal locations differ significantly, resulting in the difference in wind power density. The Weibull and lognormal distributions are applied to fit the yearly wind speeds. The lognormal distribution performs better than the Weibull distribution at 8 coastal stations according to two judgement criteria, the Kolmogorov–Smirnov test and absolute error (AE). Regarding the annual maximum extreme wind speed, the generalized extreme value (GEV) distribution performs better than the commonly-used Gumbel distribution. At these southeastern coastal locations, strong winds usually occur in typhoon season. These 4 coastal provinces, that is, Guangdong, Fujian, Hainan, and Zhejiang, which have abundant wind resources, are also prone to typhoon disasters. PMID:26313256

  7. Floating marine debris in coastal waters of the SE-Pacific (Chile).

    PubMed

    Thiel, M; Hinojosa, I; Vásquez, N; Macaya, E

    2003-02-01

    Herein we report on the abundance and composition of floating marine debris (FMD) in coastal waters of the SE-Pacific (off the Chilean coast) during the austral summer 2002. The observed FMD consisted mainly of plastic material (86.9%). Densities of FMD were highest between 20 degrees S and 40 degrees S, corresponding to the main concentrations of human population and activities. Low densities of FMD were found in the south between 40 degrees S and 50 degrees S (<1 item km(-2)). Generally, the highest densities were recorded in nearshore waters of major port cities (>20 items km(-2)), but occasionally high concentrations of debris were also found 50 km offshore. Densities of FMD in coastal waters of the SE-Pacific are of similar magnitudes as those found in coastal waters or inland seas of highly populated regions in the northern hemisphere, indicating the need for improved regulation and legislation in the countries of the SE-Pacific.

  8. Spatial distribution of dinoflagellates from the tropical coastal waters of the South Andaman, India: Implications for coastal pollution monitoring.

    PubMed

    Narale, Dhiraj Dhondiram; Anil, Arga Chandrashekar

    2017-02-15

    Dinoflagellate community structure from two semi-enclosed areas along the South Andaman region, India, was investigated to assess the anthropogenic impact on coastal water quality. At the densely inhabited Port Blair Bay, the dominance of mixotrophs in water and Protoperidinoids in sediments was attributed to anthropogenic nutrient enrichment and prey availability. A significant decrease in dinoflagellate abundance from inner to outer bay emphasize the variation in nutrient availability. The dominance of autotrophs and Gonyaulacoid cysts at the North Bay highlight low nutrient conditions with less anthropogenic pressure. The occurrence of oceanic Ornithocercus steinii and Diplopsalis sp. could evince the oceanic water intrusion into the North Bay. Nine potentially harmful and red-tide-forming species including Alexandrium tamarense complex, A. minutum were identified in this study. Although there are no harmful algal bloom (HABs) incidences in this region so far, increasing coastal pollution could support their candidature towards the future HABs initiation and development. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women

    PubMed Central

    Garland, Suzanne M.; Fairley, Christopher K.; Hocking, Jane S.; Law, Matthew G.; Plummer, Erica L.; Fethers, Katherine A.; Chow, Eric P. F.; Tabrizi, Sepehr N.; Bradshaw, Catriona S.

    2017-01-01

    Objectives To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. Methods Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. Results A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (p<0.030); sexual activity did not influence consistency. Women who developed BV were more likely to have clade GV4 compared to those reporting no sex/practiced non-coital activities (OR = 11.82, 95%CI:1.87,74.82,p = 0.009). Specimens were more likely to contain multiple G.vaginalis clades rather than a single clade if women engaged in penile-vaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). Conclusions Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially

  10. The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women.

    PubMed

    Vodstrcil, Lenka A; Twin, Jimmy; Garland, Suzanne M; Fairley, Christopher K; Hocking, Jane S; Law, Matthew G; Plummer, Erica L; Fethers, Katherine A; Chow, Eric P F; Tabrizi, Sepehr N; Bradshaw, Catriona S

    2017-01-01

    To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (p<0.030); sexual activity did not influence consistency. Women who developed BV were more likely to have clade GV4 compared to those reporting no sex/practiced non-coital activities (OR = 11.82, 95%CI:1.87,74.82,p = 0.009). Specimens were more likely to contain multiple G.vaginalis clades rather than a single clade if women engaged in penile-vaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially pathogenic clades.

  11. A new methodology to assess antimicrobial resistance of bacteria in coastal waters; pilot study in a Mediterranean hydrosystem

    NASA Astrophysics Data System (ADS)

    Almakki, Ayad; Estèves, Kevin; Vanhove, Audrey S.; Mosser, Thomas; Aujoulat, Fabien; Marchandin, Hélène; Toubiana, Mylène; Monfort, Patrick; Jumas-Bilak, Estelle; Licznar-Fajardo, Patricia

    2017-10-01

    The global resistome of coastal waters has been less studied than that of other waters, including marine ones. Here we develop an original method for characterizing the antimicrobial resistance of bacterial communities in coastal waters. The method combines the determination of a new parameter, the community Inhibitory Concentration (c-IC) of antibiotics (ATBs), and the description of the taxonomic richness of the resistant bacteria. We test the method in a Mediterranean hydrosystem, in the Montpellier region, France. Three types of waters are analyzed: near coastal river waters (Lez), lagoon brackish waters (Mauguio), and lake freshwaters (Salagou). Bacterial communities are grown in vitro in various conditions of temperature, salinity, and ATB concentrations. From these experiments, we determine the concentrations of ATB that decrease the bacterial community abundance by 50% (c-IC50) and by 90% (c-IC90). In parallel, we determine the taxonomic repertory of the resistant growing bacteria communities (repertory of Operational Taxonomic Units [OTU]). Temperature and salinity influence the abundance of the cultivable bacteria in presence of ATBs and hence the c-ICs. Very low ATB concentrations can decrease the bacterial abundance significantly. Beside a few ubiquitous genera (Bacillus, Pseudomonas, Shewanella, Vibrio), most resistant OTUs are specific of a type of water. In brackish water, resistant OTUs are more diverse and their community structure less vulnerable to ATBs than those in freshwater. We anticipate that c-IC measurement combined with taxonomic description can be applied to any littoral region to characterize the resistant bacterial communities in the coastal waters. This would help us to evaluate the vulnerability of aquatic ecosystems to antimicrobial pressure.

  12. Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

    ERIC Educational Resources Information Center

    Codella, Sylvio G.

    2002-01-01

    Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

  13. Controls of picophytoplankton abundance and composition in a highly dynamic marine system, the Northern Alboran Sea (Western Mediterranean)

    NASA Astrophysics Data System (ADS)

    Amorim, Ana L.; León, Pablo; Mercado, Jesús M.; Cortés, Dolores; Gómez, Francisco; Putzeys, Sebastien; Salles, Soluna; Yebra, Lidia

    2016-06-01

    The Alboran Sea is a highly dynamic basin which exhibits a high spatio-temporal variability of hydrographic structures (e.g. fronts, gyres, coastal upwellings). This work compares the abundance and composition of picophytoplankton observed across the northern Alboran Sea among eleven cruises between 2008 and 2012 using flow cytometry. We evaluate the seasonal and longitudinal variability of picophytoplankton on the basis of the circulation regimes at a regional scale and explore the presence of cyanobacteria ecotypes in the basin. The maximal abundances obtained for Prochlorococcus, Synechococcus and picoeukaryotes (12.7 × 104, 13.9 × 104 and 8.6 × 104 cells mL- 1 respectively) were consistent with those reported for other adjacent marine areas. Seasonal changes in the abundance of the three picophytoplankton groups were highly significant although they did not match the patterns described for other coastal waters. Higher abundances of Prochlorococcus were obtained in autumn-winter while Synechococcus and picoeukaryotes exhibited a different seasonal abundance pattern depending on the sector (e.g. Synechococcus showed higher abundance in summer in the west sector and during winter in the eastern study area). Additionally, conspicuous longitudinal gradients were observed for Prochlorococcus and Synechococcus, with Prochlorococcus decreasing from west to east and Synechococcus following the opposite pattern. The analysis of environmental variables (i.e. temperature, salinity and inorganic nutrients) and cell abundances indicates that Prochlorococcus preferred high salinity and nitrate to phosphate ratio. On the contrary, temperature did not seem to play a role in Prochlorococcus distribution as it was numerically important during the whole seasonal cycle. Variability in Synechococcus abundance could not be explained by changes in any environmental variable suggesting that different ecotypes were sampled during the surveys. In particular, our data would indicate

  14. Characterizing mercury concentrations and flux dynamics in a coastal plain watershed using multiple models and data

    EPA Science Inventory

    Mercury-related fish consumption advisories are widespread in the coastal plain of the southeastern U.S., where atmospherically deposited mercury interacts with an abundance of wetlands and high-dissolved organic carbon (DOC), acidic waters. Recent trends in decision making proce...

  15. Sustainable Development of Philippine Coastal Resources: Subsidiarity in Ethnoecology through Inclusive Participatory Education

    ERIC Educational Resources Information Center

    Ayala, Joey; Bautista, Pauline; Pajaro, Marivic; Raquino, Mark; Watts, Paul

    2016-01-01

    The Philippines is an archipelago of more than 7,100 islands, with a population of over 100 million people dependent upon marine resources which are characterised by a decline in both biodiversity and abundance. The resultant large sector of fisherfolk is generally impoverished with limited education, which makes coastal adult education and…

  16. The Three Clades of the Telomere-Associated TLO Gene Family of Candida albicans Have Different Splicing, Localization, and Expression Features

    PubMed Central

    Anderson, Matthew Z.; Baller, Joshua A.; Dulmage, Keely; Wigen, Lauren

    2012-01-01

    Candida albicans grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated TLO gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in C. albicans. This correlates with increased virulence and clinical prevalence relative to those of other Candida clade species. The 14 expressed TLO gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally, TLOα genes are generally expressed at much higher levels than are TLOγ genes. We propose that expansion of the TLO gene family and the predicted role of Tlo proteins in transcription regulation provide C. albicans with the ability to adapt rapidly to the broad range of different environmental niches within the human host. PMID:22923044

  17. Quantifying variation in speciation and extinction rates with clade data.

    PubMed

    Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

    2013-12-01

    High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  18. Revision of the Maddenia clade of Prunus (Rosaceae)

    PubMed Central

    Wen, Jun; Shi, Wenting

    2012-01-01

    Abstract The Maddenia clade of Prunus L. is monographed based on herbarium and field studies. Four species are currently accepted in this group: Prunus himalayana J.Wen, Prunus hypoleuca (Koehne) J.Wen, Prunus hypoxantha (Koehne) J.Wen, and Prunus gongshanensis J.Wen, with the last described herein as a new species. Maddenia fujianensis Y.T.Chang and Maddenia incisoserrata T.T.Yü & T.C.Ku are treated as synonyms of Prunus hypoleuca. PMID:22577333

  19. Abundance of genes involved in mercury methylation in oceanic environments

    NASA Astrophysics Data System (ADS)

    Palumbo, A. V.; Podar, M.; Gilmour, C. C.; Brandt, C. C.; Brown, S. D.; Crable, B. R.; Weighill, D.; Jacobson, D. A.; Somenahally, A. C.; Elias, D. A.

    2016-02-01

    The distribution and diversity of genes involved in mercury methylation in oceanic environments is of interest in determining the source of mercury in ocean environments and may have predictive value for mercury methylation rates. The highly conserved hgcAB genes involved in mercury methylation provide an avenue for evaluating the genetic potential for mercury methylation. The genes are sporadically present in a few diverse groups of bacteria and Archaea including Deltaproteobacteria, Firmicutes and Archaea and of over 7000 sequenced species they are only present in about 100 genomes. Examination of sequence data from methylators and non-methylators indicates that these genes are associated with other genes involved in metal transformations and transport. We examined hgcAB presence in over 3500 microbial metagenomes (from all environments) and found the hgcAB genes were present in anaerobic oceanic environments but not in aerobic layers of the open ocean. The genes were common in sediments from marine, coastal and estuarine sources as well as polluted environments. The genes were rare, found in 7 of 138 samples, in metagenomes from the pelagic water column including profiles though the oxygen minimum zone. Other oxic and sub-oxic coastal waters also demonstrated a lack of hgcAB genes including the OMZ in the Eastern North Pacific Ocean. There were some unique hgcA like unique sequences found in metagenomes from depth in the Pacific and Southern Atlantic Ocean. Coastal "dead zone" waters may be important sources of MeHg as the hgcAB genes were abundant in the anoxic waters of a stratified fjord. The genes were absent in microbiomes from vertebrates but were in invertebrate microbiomes However, oceanic species were underrepresented in these samples. Climate change could provide an additional flux of MeHg to the oceans as we found the most abundant representation of hgcAB genes in arctic permafrost. Thus warming could increase flux of methyl mercury to arctic waters.

  20. Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades

    PubMed Central

    Bachvaroff, Tsvetan R.; Gornik, Sebastian G.; Concepcion, Gregory T.; Waller, Ross F.; Mendez, Gregory S.; Lippmeier, J. Casey; Delwiche, Charles F.

    2014-01-01

    The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these ‘protist’ taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates. PMID:24135237

  1. Google Haul Out: Earth Observation Imagery and Digital Aerial Surveys in Coastal Wildlife Management and Abundance Estimation

    PubMed Central

    Moxley, Jerry H.; Bogomolni, Andrea; Hammill, Mike O.; Moore, Kathleen M. T.; Polito, Michael J.; Sette, Lisa; Sharp, W. Brian; Waring, Gordon T.; Gilbert, James R.; Halpin, Patrick N.; Johnston, David W.

    2017-01-01

    Abstract As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances. PMID:29599542

  2. Google Haul Out: Earth Observation Imagery and Digital Aerial Surveys in Coastal Wildlife Management and Abundance Estimation.

    PubMed

    Moxley, Jerry H; Bogomolni, Andrea; Hammill, Mike O; Moore, Kathleen M T; Polito, Michael J; Sette, Lisa; Sharp, W Brian; Waring, Gordon T; Gilbert, James R; Halpin, Patrick N; Johnston, David W

    2017-08-01

    As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances.

  3. Abundance and Genetic Diversity of Aerobic Anoxygenic Phototrophic Bacteria of Coastal Regions of the Pacific Ocean

    PubMed Central

    Ritchie, Anna E.

    2012-01-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by the pufM gene biomarker, are most abundant near shore and in areas with high chlorophyll or Synechococcus abundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and uncultured pufM gene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities. PMID:22307290

  4. Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

    PubMed

    Fonseca, Luiz Henrique M; Lohmann, Lúcia G

    2018-06-01

    Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Antigenic diversity of H5 highly pathogenic avian influenza viruses of clade 2.3.4.4 isolated in Asia.

    PubMed

    Ohkawara, Ayako; Okamatsu, Masatoshi; Ozawa, Makoto; Chu, Duc-Huy; Nguyen, Lam Thanh; Hiono, Takahiro; Matsuno, Keita; Kida, Hiroshi; Sakoda, Yoshihiro

    2017-05-01

    H5 highly pathogenic avian influenza viruses (HPAIV) have spread in both poultry and wild birds since late 2003. Continued circulation of HPAIV in poultry in several regions of the world has led to antigenic drift. In the present study, we analyzed the antigenic properties of H5 HPAIV isolated in Asia using four neutralizing mAbs recognizing hemagglutinin, which were established using A/chicken/Kumamoto/1-7/2014 (H5N8), belonging to clade 2.3.4.4 and also using polyclonal antibodies. Viruses of clades 1.1, 2.3.2.1, 2.3.4, and 2.3.4.4 had different reactivity patterns to the panel of mAbs, thereby indicating that the antigenicity of the viruses of clade 2.3.4.4 were similar but differed from the other clades. In particular, the antigenicity of the viruses of clade 2.3.4.4 differed from those of the viruses of clades 2.3.4 and 2.3.2.1, which suggests that the recent H5 HPAIV have further evolved antigenically divergent. In addition, reactivity of antiserum suggests that the antigenicity of viruses of clade 2.3.4.4 differed slightly among groups A, B, and C. Vaccines are still used in poultry in endemic countries, so the antigenicity of H5 HPAIV should be monitored continually to facilitate control of avian influenza. The panel of mAbs established in the present study will be useful for detecting antigenic drift in the H5 viruses that emerge from the current strains. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

  6. Repeated climate-linked host shifts have promoted diversification in a temperate clade of leaf-mining flies

    PubMed Central

    Winkler, Isaac S.; Mitter, Charles; Scheffer, Sonja J.

    2009-01-01

    A central but little-tested prediction of “escape and radiation” coevolution is that colonization of novel, chemically defended host plant clades accelerates insect herbivore diversification. That theory, in turn, exemplifies one side of a broader debate about the relative influence on clade dynamics of intrinsic (biotic) vs. extrinsic (physical-environmental) forces. Here, we use a fossil-calibrated molecular chronogram to compare the effects of a major biotic factor (repeated shift to a chemically divergent host plant clade) and a major abiotic factor (global climate change) on the macroevolutionary dynamics of a large Cenozoic radiation of phytophagous insects, the leaf-mining fly genus Phytomyza (Diptera: Agromyzidae). We find one of the first statistically supported examples of consistently elevated net diversification accompanying shift to new plant clades. In contrast, we detect no significant direct effect on diversification of major global climate events in the early and late Oligocene. The broader paleoclimatic context strongly suggests, however, that climate change has at times had a strong indirect influence through its effect on the biotic environment. Repeated rapid Miocene radiation of these flies on temperate herbaceous asterids closely corresponds to the dramatic, climate-driven expansion of seasonal, open habitats. PMID:19805134

  7. Echolocation by the harbour porpoise: life in coastal waters.

    PubMed

    Miller, Lee A; Wahlberg, Magnus

    2013-01-01

    The harbor porpoise is one of the smallest and most widely spread of all toothed whales. They are found abundantly in coastal waters all around the northern hemisphere. They are among the 11 species known to use high frequency sonar of relative narrow bandwidth. Their narrow biosonar beam helps isolate echoes from prey among those from unwanted items and noise. Obtaining echoes from small objects like net mesh, net floats, and small prey is facilitated by the very high peak frequency around 130 kHz with a wavelength of about 12 mm. We argue that such echolocation signals and narrow band auditory filters give the harbor porpoise a selective advantage in a coastal environment. Predation by killer whales and a minimum noise region in the ocean around 130 kHz may have provided selection pressures for using narrow bandwidth high frequency biosonar signals.

  8. Gulf Atlantic Coastal Plain Long Term Agroecosystem Research site, Tifton, GA

    Treesearch

    Timothy Strickland; David D. Bosch; Dinku M. Endale; Thomas L. Potter

    2016-01-01

    The Gulf-Atlantic Coastal Plain (GACP) physiographic region is an important agricultural production area within the southeastern U.S. that extends from Delaware in the Northeast to the Gulf Coast of Texas. The region consists mainly of low-elevation flat to rolling terrain with numerous streams, abundant rainfall, a complex coastline, and many wetlands. The GACP Long ...

  9. Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets.

    PubMed

    Pearce, Melissa B; Pappas, Claudia; Gustin, Kortney M; Davis, C Todd; Pantin-Jackwood, Mary J; Swayne, David E; Maines, Taronna R; Belser, Jessica A; Tumpey, Terrence M

    2017-02-01

    Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. Published by Elsevier Inc.

  10. Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets

    PubMed Central

    Pearce, Melissa B.; Pappas, Claudia; Gustin, Kortney M.; Davis, C. Todd; Pantin-Jackwood, Mary J.; Swayne, David E.; Maines, Taronna R.; Belser, Jessica A.; Tumpey, Terrence M.

    2017-01-01

    Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2 A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2 A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. PMID:28038412

  11. Distinct Processes Drive Diversification in Different Clades of Gesneriaceae.

    PubMed

    Roalson, Eric H; Roberts, Wade R

    2016-07-01

    Using a time-calibrated phylogenetic hypothesis including 768 Gesneriaceae species (out of [Formula: see text]3300 species) and more than 29,000 aligned bases from 26 gene regions, we test Gesneriaceae for diversification rate shifts and the possible proximal drivers of these shifts: geographic distributions, growth forms, and pollination syndromes. Bayesian Analysis of Macroevolutionary Mixtures analyses found five significant rate shifts in Beslerieae, core Nematanthus, core Columneinae, core Streptocarpus, and Pacific Cyrtandra These rate shifts correspond with shifts in diversification rates, as inferred by Binary State Speciation and Extinction Model and Geographic State Speciation and Extinction model, associated with hummingbird pollination, epiphytism, unifoliate growth, and geographic area. Our results suggest that diversification processes are extremely variable across Gesneriaceae clades with different combinations of characters influencing diversification rates in different clades. Diversification patterns between New and Old World lineages show dramatic differences, suggesting that the processes of diversification in Gesneriaceae are very different in these two geographic regions. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Abundance and Genetic Diversity of Microbial Polygalacturonase and Pectate Lyase in the Sheep Rumen Ecosystem

    PubMed Central

    Wang, Yaru; Luo, Huiying; Huang, Huoqing; Shi, Pengjun; Bai, Yingguo; Yang, Peilong; Yao, Bin

    2012-01-01

    Background Efficient degradation of pectin in the rumen is necessary for plant-based feed utilization. The objective of this study was to characterize the diversity, abundance, and functions of pectinases from microorganisms in the sheep rumen. Methodology/Principal Findings A total of 103 unique fragments of polygalacturonase (PF00295) and pectate lyase (PF00544 and PF09492) genes were retrieved from microbial DNA in the rumen of a Small Tail Han sheep, and 66% of the sequences of these fragments had low identities (<65%) with known sequences. Phylogenetic tree building separated the PF00295, PF00544, and PF09492 sequences into five, three, and three clades, respectively. Cellulolytic and noncellulolytic Butyrivibrio, Prevotella, and Fibrobacter species were the major sources of the pectinases. The two most abundant pectate lyase genes were cloned, and their protein products, expressed in Escherichia coli, were characterized. Both enzymes probably act extracellularly as their nucleotide sequences contained signal sequences, and they had optimal activities at the ruminal physiological temperature and complementary pH-dependent activity profiles. Conclusion/Significance This study reveals the specificity, diversity, and abundance of pectinases in the rumen ecosystem and provides two additional ruminal pectinases for potential industrial use under physiological conditions. PMID:22815874

  13. Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound.

    PubMed

    Lee, Timothy S; Toft, Jason D; Cordell, Jeffery R; Dethier, Megan N; Adams, Jeffrey W; Kelly, Ryan P

    2018-01-01

    Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic-terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness) from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable.

  14. Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound

    PubMed Central

    Toft, Jason D.; Adams, Jeffrey W.

    2018-01-01

    Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic–terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness) from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable. PMID:29492331

  15. Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

    PubMed Central

    2012-01-01

    Background The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium) is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community) with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D). Results We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via ‘shuffling’ the proportions of these two clades from within their current symbiont communities. Conclusions Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg. pairwise nucleotide difference

  16. Microplastics and polycyclic aromatic hydrocarbons (PAHs) in Xiamen coastal areas: Implications for anthropogenic impacts.

    PubMed

    Tang, Guowen; Liu, Mengyang; Zhou, Qian; He, Haixia; Chen, Kai; Zhang, Haibo; Hu, Jiahui; Huang, Qinghui; Luo, Yongming; Ke, Hongwei; Chen, Bin; Xu, Xiangrong; Cai, Minggang

    2018-09-01

    Microplastics and polycyclic aromatic hydrocarbons (PAHs) were investigated to study the influence of human activities and to find their possible relationship on the coastal environments, where the coastal areas around Xiamen are undergoing intensive processes of industrialization and urbanization in the southeast China. The abundance of microplastics in Xiamen coastal areas was 103 to 2017particles/m 3 in surface seawater and 76 to 333 particles/kg in sediments. Concentrations of dissolved PAHs varied from 18.1 to 248ng/L in surface seawater. The abundances of microplastics from the Western Harbor in surface seawater and sediments were higher than those from other areas. Foams were dominated in surface seawater samples, however, no foams were found in sediments samples. The microscope selection and FTIR analysis suggested that polyethylene (PE) and polypropylene (PP) were dominant microplastics. The cluster analysis results demonstrated that fibers and granules had the similar sources, and films had considerably correlation with all types of PAHs (3 or 4-ring PAHs and alkylated PAHs). Plastic film mulch from agriculture practice might be a potential source of microplastics in study areas. Results of our study support that river runoff, watershed area, population and urbanization rate influence the distribution of microplastics in estuarine surface water, and the prevalence of microplastic pollution calls for monitoring microplastics at a national scale. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Development of the coastal zone color scanner for NIMBUS 7. Volume 1: Mission objectives and instrument description

    NASA Technical Reports Server (NTRS)

    1979-01-01

    An Earth scanning six channel (detector) radiometer using a classical Cassegrain telescope and a Wadsworth type grating spectrometer was launched aboard Nimbus 7 in order to determine the abundance or density of chlorophyll at or near the sea surface in coastal waters. The instrument also measures the sediment or gelbstroffe (yellow stuff) in coastal waters, detects surface vegetation, and measures sea surface temperature. Block diagrams and schematics are presented, design features are discussed and each subsystem of the instrument is described. A mission overview is included.

  18. Seasonal changes in habitat availability and the distribution and abundance of salmonids along a stream gradient from headwaters to mouth in coastal Oregon

    Treesearch

    Gordon H. Reeves; Jack D. Sleeper; Dirk W. Lang

    2011-01-01

    Visual estimation techniques were used to quantify seasonal habitat characteristics, habitat use, and longitudinal distribution of juvenile steelhead Oncorhynchus mykiss, coastal cutthroat trout O. clarkii clarkii and coho salmon O. kisutch in a coastal Oregon basin. At the channel unit scale, fish...

  19. [Composition, distribution and abundance of gastropod larvae in the South of Quintana Roo,Mexico and north of Belice].

    PubMed

    Oliva Rivera, J; de Jesús Navarrete, A

    2000-12-01

    To know the composition, abundance and distribution of gastropod larvae, monthly samplings were carried out in the south of Quintana Roo, Mexico and north of Belize, from April to December, 1996. Collections were made in six sites at Chinchorro Bank, four in the South Coast and six at Hol-Chan, Belize, between the 10 and 20 hrs. At each station 2.5 m3 of seawater were pumped through a 202 microns mesh; 27 species were identified. The most abundant species were: South Coast, Rissoina sp. 1., Limacina sp. 1 and Natica sp. 1, Chinchorro Bank, Limacina sp. 1, Creseis acicula, Cerithiopsis hero and Rissoina sp. 1 and Hol-Chan, Limacina sp. 2, Alaba incerta and Rissoina sp. 1. The highest abundance was in rainy season. Apparently the presence of winds, coastal currents and food availability, control the distribution and abundance of larvae.

  20. Novel H5N8 clade 2.3.4.4 highly pathogenic avian influenza virus in wild awuatic birds, Russia, 2016

    USDA-ARS?s Scientific Manuscript database

    H5N1 high pathogenicity avian influenza virus (HPAIV) emerged in 1996 in Guangdong China (Gs/GD) and has evolved into multiple genetic clades. Since 2008, HPAIV H5 clade 2.3.4 with N2, N5 and N8 neuraminidase subtypes have been identified in mainland China and outbreak of HPAIV H5N8 clade 2.3.4.4 ou...

  1. Marine litter in the upper São Vicente submarine canyon (SW Portugal): Abundance, distribution, composition and fauna interactions.

    PubMed

    Oliveira, Frederico; Monteiro, Pedro; Bentes, Luis; Henriques, Nuno Sales; Aguilar, Ricardo; Gonçalves, Jorge M S

    2015-08-15

    Marine litter has become a worldwide environmental problem, tainting all ocean habitats. The abundance, distribution and composition of litter and its interactions with fauna were evaluated in the upper S. Vicente canyon using video images from 3 remote operated vehicle exploratory dives. Litter was present in all dives and the abundance was as high as 3.31 items100m(-1). Mean abundance of litter over rock bottom was higher than on soft substrate. Mean litter abundance was slightly higher than reported for other canyons on the Portuguese margin, but lower in comparison to more urbanized coastal areas of the world. Lost fishing gear was the prevalent type of litter, indicating that the majority of litter originates from maritime sources, mainly fishing activity. Physical contact with sessile fauna and entanglement of specimens were the major impacts of lost fishing gear. Based on the importance of this region for the local fishermen, litter abundance is expected to increase. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

    PubMed Central

    Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  3. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    PubMed

    Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

  4. Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify MLST clade 4 Clostridium difficile isolates.

    PubMed

    Cheng, Jing-Wei; Liu, Chang; Kudinha, Timothy; Xiao, Meng; Yu, Shu-Ying; Yang, Chun-Xia; Wei, Ming; Liang, Guo-Wei; Shao, Dong-Hua; Kong, Fanrong; Tong, Zhao-Hui; Xu, Ying-Chun

    2018-04-26

    Clostridium difficile is the leading cause of health care-associated infections. Previous studies suggest that C. difficile MLST clade 4 strains with higher drug resistance rates constitute the major clone spreading in China. Thus development of a rapid and accurate typing method for these strains is needed to monitor the epidemiology of this clone and to guide clinical treatment. A total of 160 non-duplicate C. difficile isolates recovered from three large teaching hospitals in Beijing were studied. All the 41 clade 4 C. difficile isolates clustered together on the PCA dendrogram. Spectra peak statistics revealed that five markers (2691.43Da, 2704.91Da, 2711.93Da, 3247.27Da and 3290.76Da) can easily and reliably distinguish between clade 4 and non-clade 4 isolates, with area under the curve (AUC) values of 0.991, 0.997, 0.973, 1 and 1, respectively. In conclusion, MALDI-TOF MS is a very simple and accurate method for identifying C. difficile MLST clade 4 strains. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Molecular phylogeny of the spider family Sparassidae with focus on the genus Eusparassus and notes on the RTA-clade and 'Laterigradae'.

    PubMed

    Moradmand, Majid; Schönhofer, Axel L; Jäger, Peter

    2014-05-01

    The phylogeny of the spider family Sparassidae is comprehensively investigated using four molecular markers (mitochondrial COI and 16S; nuclear H3 and 28S). Sparassidae was recovered as monophyletic and as most basal group within the RTA-clade. The higher-level clade Dionycha was not but monophyly of RTA-clade was supported. No affiliation of Sparassidae to other members of the 'Laterigradae' (Philodromidae, Selenopidae and Thomisidae) was observed, and the crab-like posture of this group assumed a result of convergent evolution. Only Philodromidae and Selenopidae were found members of a supported clade, but together with Salticidae and Corinnidae, while Thomisidae was nested within the higher Lycosoidea. Within Sparassidae monophyly of the subfamilies Heteropodinae sensu stricto, Palystinae and Deleninae was recovered. Sparianthinae was supported as the most basal clade within Sparassidae. Sparassinae and the genus Olios were found each to be polyphyletic. Eusparassinae was not recovered monophyletic, with the two original genera Eusparassus and Pseudomicrommata in separate clades and only the latter clustered with most other assumed Eusparassinae, here termed the "African clade". Further focus was on the monophyletic genus Eusparassus and its proposed species groups, of which the dufouri-, walckenaeri- and doriae-group were confirmed as monophyletic with the two latter groups more closely related. According to molecular clock analyses, the divergence time of Sparassidae and Eusparassus was estimated with 186 and 70 million years ago respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Meiobenthic communities in permanently open estuaries and open/closed coastal lagoons of Uruguay (Atlantic coast of South America)

    NASA Astrophysics Data System (ADS)

    Kandratavicius, N.; Muniz, P.; Venturini, N.; Giménez, L.

    2015-09-01

    This study aimed to determine if estuarine meiofaunal communities of Uruguay (South America) vary between permanently open estuaries and open/closed coastal lagoons, or if they respond to the sediment composition. In Uruguay, estuaries and coastal lagoons vary in the degree of connectivity to the sea and in the sediment composition; sediments in estuaries are characterized by fine-medium sands but sediments vary from lagoon to lagoon (either fine-medium or coarse sand). Taxa richness (total = 16) showed less temporal variability in lagoons than in estuaries, due to patterns of presence/absence of the less abundant taxa. However, no major response to habitat was found in the most abundant groups: polychaetes (6% of total fauna) were on average 5% more abundant in lagoons than in estuaries. Some level of zonation, within estuaries and lagoons, was found in the most abundant groups, nematodes (63% of total fauna) and copepods (15%) in response to medium and fine sands. In addition, sediment type modulated seasonal patterns in the frequency of presence/absence in ostracods, polychaetes and oligochaetes. For instance, in polychaetes and ostracods the increase in the frequency of absences, occurring from summer to winter, was stronger in lagoons and estuaries dominated by fine sands. The lagoon habitat appears to ameliorate the effects of unfavourable (winter) conditions in less abundant meiofaunal taxa. In summary, sediment fractions explain spatial patterns in the average abundance of organisms (e.g. nematodes) as well as the seasonal changes in frequency of presence/absence (e.g. polychaetes).

  7. Phytoplankton responses to atmospheric metal deposition in the coastal and open-ocean Sargasso Sea

    PubMed Central

    Mackey, Katherine R. M.; Buck, Kristen N.; Casey, John R.; Cid, Abigail; Lomas, Michael W.; Sohrin, Yoshiki; Paytan, Adina

    2012-01-01

    This study investigated the impact of atmospheric metal deposition on natural phytoplankton communities at open-ocean and coastal sites in the Sargasso Sea during the spring bloom. Locally collected aerosols with different metal contents were added to natural phytoplankton assemblages from each site, and changes in nitrate, dissolved metal concentration, and phytoplankton abundance and carbon content were monitored. Addition of aerosol doubled the concentrations of cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), and nickel (Ni) in the incubation water. Over the 3-day experiments, greater drawdown of dissolved metals occurred in the open ocean water, whereas little metal drawdown occurred in the coastal water. Two populations of picoeukaryotic algae and Synechococcus grew in response to aerosol additions in both experiments. Particulate organic carbon increased and was most sensitive to changes in picoeukaryote abundance. Phytoplankton community composition differed depending on the chemistry of the aerosol added. Enrichment with aerosol that had higher metal content led to a 10-fold increase in Synechococcus abundance in the oceanic experiment but not in the coastal experiment. Enrichment of aerosol-derived Co, Mn, and Ni were particularly enhanced in the oceanic experiment, suggesting the Synechococcus population may have been fertilized by these aerosol metals. Cu-binding ligand concentrations were in excess of dissolved Cu in both experiments, and increased with aerosol additions. Bioavailable free hydrated Cu2+ concentrations were below toxicity thresholds throughout both experiments. These experiments show (1) atmospheric deposition contributes biologically important metals to seawater, (2) these metals are consumed over time scales commensurate with cell growth, and (3) growth responses can differ between distinct Synechococcus or eukaryotic algal populations despite their relatively close geographic proximity and taxonomic similarity. PMID

  8. Environmental dynamics of red Noctiluca scintillans bloom in tropical coastal waters.

    PubMed

    Baliarsingh, S K; Lotliker, Aneesh A; Trainer, Vera L; Wells, Mark L; Parida, Chandanlal; Sahu, Biraja K; Srichandan, Suchismita; Sahoo, Subhashree; Sahu, K C; Kumar, T Sinivasa

    2016-10-15

    An intense bloom of red Noctiluca scintillans (NS) occurred off the Rushikulya estuarine region along the east coast of India, an important site for mass nesting events of the vulnerable Olive Ridley sea turtle. At its peak, densities of NS were 3.3×10(5) cells-l(-1), with low relative abundance of other phytoplankton. The peak bloom coincided with high abundance of gelatinous planktivores which may have facilitated bloom development by their grazing on other zooplankton, particularly copepods. Ammonium concentrations increased by approximately 4-fold in the later stages of bloom, coincident with stable NS abundance and chlorophyll concentrations in the nano- and microplankton. This increase likely was attributable to release of intracellular ammonium accumulated through NS grazing. Dissolved oxygen concentrations decreased in sub-surface waters to near hypoxia. Micro-phytoplankton increasingly dominated chlorophyll-a biomass as the bloom declined, with diminishing picoplankton abundance likely the result of high predation by the ciliate Mesodinium rubrum. Together, these data illustrate factors that can disrupt ecosystem balance in this critically important Indian coastal region. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Interactive network configuration maintains bacterioplankton community structure under elevated CO2 in a eutrophic coastal mesocosm experiment

    NASA Astrophysics Data System (ADS)

    Lin, Xin; Huang, Ruiping; Li, Yan; Li, Futian; Wu, Yaping; Hutchins, David A.; Dai, Minhan; Gao, Kunshan

    2018-01-01

    There is increasing concern about the effects of ocean acidification on marine biogeochemical and ecological processes and the organisms that drive them, including marine bacteria. Here, we examine the effects of elevated CO2 on the bacterioplankton community during a mesocosm experiment using an artificial phytoplankton community in subtropical, eutrophic coastal waters of Xiamen, southern China. Through sequencing the bacterial 16S rRNA gene V3-V4 region, we found that the bacterioplankton community in this high-nutrient coastal environment was relatively resilient to changes in seawater carbonate chemistry. Based on comparative ecological network analysis, we found that elevated CO2 hardly altered the network structure of high-abundance bacterioplankton taxa but appeared to reassemble the community network of low abundance taxa. This led to relatively high resilience of the whole bacterioplankton community to the elevated CO2 level and associated chemical changes. We also observed that the Flavobacteria group, which plays an important role in the microbial carbon pump, showed higher relative abundance under the elevated CO2 condition during the early stage of the phytoplankton bloom in the mesocosms. Our results provide new insights into how elevated CO2 may influence bacterioplankton community structure.

  10. Echolocation by the harbour porpoise: life in coastal waters

    PubMed Central

    Miller, Lee A.; Wahlberg, Magnus

    2013-01-01

    The harbor porpoise is one of the smallest and most widely spread of all toothed whales. They are found abundantly in coastal waters all around the northern hemisphere. They are among the 11 species known to use high frequency sonar of relative narrow bandwidth. Their narrow biosonar beam helps isolate echoes from prey among those from unwanted items and noise. Obtaining echoes from small objects like net mesh, net floats, and small prey is facilitated by the very high peak frequency around 130 kHz with a wavelength of about 12 mm. We argue that such echolocation signals and narrow band auditory filters give the harbor porpoise a selective advantage in a coastal environment. Predation by killer whales and a minimum noise region in the ocean around 130 kHz may have provided selection pressures for using narrow bandwidth high frequency biosonar signals. PMID:23596420

  11. Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

    NASA Astrophysics Data System (ADS)

    He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

    2017-04-01

    Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

  12. Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

    NASA Astrophysics Data System (ADS)

    He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

    2018-03-01

    Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

  13. Characteristics of Aedes aegypti adult mosquitoes in rural and urban areas of western and coastal Kenya

    PubMed Central

    Ndenga, Bryson Alberto; Mutuku, Francis Maluki; Ngugi, Harun Njenga; Mbakaya, Joel Omari; Aswani, Peter; Musunzaji, Peter Siema; Vulule, John; Mukoko, Dunstan; Kitron, Uriel; LaBeaud, Angelle Desiree

    2017-01-01

    Aedes aegypti is the main vector for yellow fever, dengue, chikungunya and Zika viruses. Recent outbreaks of dengue and chikungunya have been reported in Kenya. Presence and abundance of this vector is associated with the risk for the occurrence and transmission of these diseases. This study aimed to characterize the presence and abundance of Ae. aegypti adult mosquitoes from rural and urban sites in western and coastal regions of Kenya. Presence and abundance of Ae. aegypti adult mosquitoes were determined indoors and outdoors in two western (urban Kisumu and rural Chulaimbo) and two coastal (urban Ukunda and rural Msambweni) sites in Kenya. Sampling was performed using quarterly human landing catches, monthly Prokopack automated aspirators and monthly Biogents-sentinel traps. A total of 2,229 adult Ae. aegypti mosquitoes were collected: 785 (35.2%) by human landing catches, 459 (20.6%) by Prokopack aspiration and 985 (44.2%) by Biogents-sentinel traps. About three times as many Ae. aegypti mosquitoes were collected in urban than rural sites (1,650 versus 579). Comparable numbers were collected in western (1,196) and coastal (1,033) sites. Over 80% were collected outdoors through human landing catches and Prokopack aspiration. The probability of collecting Ae. aegypti mosquitoes by human landing catches was significantly higher in the afternoon than morning hours (P<0.001), outdoors than indoors (P<0.001) and in urban than rural sites (P = 0.008). Significantly more Ae. aegypti mosquitoes were collected using Prokopack aspiration outdoors than indoors (P<0.001) and in urban than rural areas (P<0.001). Significantly more mosquitoes were collected using Biogents-sentinel traps in urban than rural areas (P = 0.008) and in western than coastal sites (P = 0.006). The probability of exposure to Ae. aegypti bites was highest in urban areas, outdoors and in the afternoon hours. These characteristics have major implications for the possible transmission of arboviral

  14. Characteristics of Aedes aegypti adult mosquitoes in rural and urban areas of western and coastal Kenya.

    PubMed

    Ndenga, Bryson Alberto; Mutuku, Francis Maluki; Ngugi, Harun Njenga; Mbakaya, Joel Omari; Aswani, Peter; Musunzaji, Peter Siema; Vulule, John; Mukoko, Dunstan; Kitron, Uriel; LaBeaud, Angelle Desiree

    2017-01-01

    Aedes aegypti is the main vector for yellow fever, dengue, chikungunya and Zika viruses. Recent outbreaks of dengue and chikungunya have been reported in Kenya. Presence and abundance of this vector is associated with the risk for the occurrence and transmission of these diseases. This study aimed to characterize the presence and abundance of Ae. aegypti adult mosquitoes from rural and urban sites in western and coastal regions of Kenya. Presence and abundance of Ae. aegypti adult mosquitoes were determined indoors and outdoors in two western (urban Kisumu and rural Chulaimbo) and two coastal (urban Ukunda and rural Msambweni) sites in Kenya. Sampling was performed using quarterly human landing catches, monthly Prokopack automated aspirators and monthly Biogents-sentinel traps. A total of 2,229 adult Ae. aegypti mosquitoes were collected: 785 (35.2%) by human landing catches, 459 (20.6%) by Prokopack aspiration and 985 (44.2%) by Biogents-sentinel traps. About three times as many Ae. aegypti mosquitoes were collected in urban than rural sites (1,650 versus 579). Comparable numbers were collected in western (1,196) and coastal (1,033) sites. Over 80% were collected outdoors through human landing catches and Prokopack aspiration. The probability of collecting Ae. aegypti mosquitoes by human landing catches was significantly higher in the afternoon than morning hours (P<0.001), outdoors than indoors (P<0.001) and in urban than rural sites (P = 0.008). Significantly more Ae. aegypti mosquitoes were collected using Prokopack aspiration outdoors than indoors (P<0.001) and in urban than rural areas (P<0.001). Significantly more mosquitoes were collected using Biogents-sentinel traps in urban than rural areas (P = 0.008) and in western than coastal sites (P = 0.006). The probability of exposure to Ae. aegypti bites was highest in urban areas, outdoors and in the afternoon hours. These characteristics have major implications for the possible transmission of arboviral

  15. Stratigraphy of Atlantic coastal margin of United States north of Cape Hatteras; brief survey

    USGS Publications Warehouse

    Perry, W.J.; Minard, J.P.; Weed, E.G.A.; Robbins, E.I.; Rhodehamel, E.C.

    1975-01-01

    A synthesis of studies of sea-floor outcrops of the sedimentary wedge beneath the northeastern United States continental shelf and slope and a reassessment of coastal plain Mesozoic stratigraphy, particularly of the coastal margin, provide insight for estimating the oil and gas potential and provide geologic control for marine seismic investigations of the Atlantic continental margin. The oldest strata known to crop out on the continental slope are late Campanian in age. The Cretaceous-Tertiary contact along the slope ranges from a water depth of 0.6 to 1.5 km south of Georges Bank to 1.8 km in Hudson Canyon. Few samples are available from Tertiary and Late Cretaceous outcrops along the slope. Sediments of the Potomac Group, chiefly of Early Cretaceous age, constitute a major deltaic sequence in the emerged coastal plain. This thick sequence lies under coastal Virginia, Maryland, Delaware, southeastern New Jersey, and the adjacent continental shelf. Marine sands associated with this deltaic sequence may be present seaward under the outer continental shelf. South of the Norfolk arch, under coastal North Carolina, carbonate rocks interfinger with Lower Cretaceous clastic strata. From all available data, Mesozoic correlations in coastal wells between coastal Virginia and Long Island have been revised. The Upper-Lower Cretaceous boundary is placed at the transition between Albian and Cenomanian floras. Potential hydrocarbon source beds are present along the coast in the subsurface sediments of Cretaceous age. Potential reservoir sandstones are abundant in this sequence.

  16. Arthropod abundance and seasonal bird use of bottomland forest harvest gaps.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moorman, Christopher, E.; Bowen, Liessa T.; Kilgo, John, C.

    2012-03-01

    We investigated the influence of arthropod abundance and vegetation structure on shifts in avian use of canopy gap, gap edge, and surrounding forest understory in a bottomland hardwood forest in the Upper Coastal Plain of South Carolina. We compared captures of foliage-gleaning birds among locations during four periods (spring migration, breeding, post-breeding, and fall migration). Foliage arthropod densities were greatest in the forest understory in all four seasons, but understory vegetation density was greatest in gaps. Foliage-gleaning bird abundance was positively associated with foliage-dwelling arthropods during the breeding (F = 18.5, P < 0.001) and post-breeding periods (F = 9.4,more » P = 0.004), and negatively associated with foliage-dwelling arthropods during fall migration (F = 5.4, P = 0.03). Relationships between birds and arthropods were inconsistent, but the arthropod prey base seemed to be least important during migratory periods. Conversely, bird captures were positively correlated with understory vegetation density during all four periods (P < 0.001). Our study suggests high bird abundance associated with canopy gaps during the non-breeding period resulted less from high arthropod food resource availability than from complex understory and midstory vegetation structure.« less

  17. Diversity and Abundance of Chlorophyta in Krakal Beach, Gunung Kidul, Yogyakarta

    NASA Astrophysics Data System (ADS)

    Putri, A. C.; Nugroho, I. C.; Firdaus, N. U. N.; Puspita, N. O. J.; Fajrin, S. A. R.; Hamzah, S. D. A.

    2017-10-01

    Chlorophyta plays an important role in energy flow as the main producer in marine food chain, material circulation, bioaccumulation, and bio-indicator in the intertidal zone. Several genera of Chlorophyta have been used by local society around coastal area of Gunung Kidul, Yogyakarta as local product, but the research about diversity and abundance information of Chlorophyta in Krakal beach was not yet understood. The aim of this study is to gain the information about diversity and abundancy of Chlorophyta in Krakal Beach, Gunung Kidul,Yogyakarta. This research was conducted in March 11th 2017. This research utilizes Line Transect and Stratified Random Sampling method which is used 1x1 m plot. There are six genera of Chlorophyta have been identified in this research, such as Chaetomorpha sp.; Boergesenia sp; Ulva sp.; Cladophora sp.; Enteromorpha sp.; and Halicystis sp. From 6 genera of Chlorophyta, the highest genera coverage is Enteromorpha sp. (9.88%). This research is expected to record data of macroalgae abundance especially Chlorophyta, in Krakal Beach. By this research, monitoring of macroalgae could be done and supported by government and local people to maintain the sustainability of Chlorophyta.

  18. Seagrass distribution and abundance in Eastern Gulf of Mexico coastal waters

    NASA Astrophysics Data System (ADS)

    Iverson, Richard L.; Bittaker, Henry F.

    1986-05-01

    The marine angiosperms Thalassia testudinum, Syringodium filiforme, and Halodule wrightii form two of the largest reported seagrass beds along the northwest and southern coasts of Florida where they cover about 3000 square km in the Big Bend area and about 5500 square km in Florida Bay, respectively. Most of the leaf biomass in the Big Bend area and outer Florida Bay was composed of Thalassia testudinum and Syringodium filiforme which were distributed throughout the beds but which were more abundant in shallow depths. A short-leaved form of Halodule wrightii grew in monotypic stands in shallow water near the inner edges of the beds, while Halophila decipiens and a longer-leaved variety of H. wrightii grew scattered throughout the beds, in monotypic stands near the outer edges of the beds, and in deeper water outside the beds. Halophila engelmanni was observed scattered at various depths throughout the seagrass beds and in monospecific patches in deep water outside the northern bed. Ruppia maritima grew primarily in brackish water around river mouths. The cross-shelf limits of the two major seagrass beds are controlled nearshore by increased water turbidity and lower salinity around river mouths and off-shore by light penetration to depths which receive 10% or more of sea surface photosynthetically active radiation. Seagrasses form large beds only along low energy reaches of the coast. The Florida Bay seagrass bed contained about twice the short-shoot density of both Thalassia testudinum and Syringodium filiforme, for data averaged over all depths, and about four times the average short-shoot density of both species in shallow water compared with the Big Bend seagrass bed. The differences in average seagrass abundance between Florida Bay and the Big Bend area may be a consequence of the effects of greater seasonal solar radiation and water temperature fluctuations experienced by plants in the northern bed, which lies at the northern distribution limit for American

  19. Results of complex annual parasitological monitoring in the coastal area of Kola Bay

    NASA Astrophysics Data System (ADS)

    Kuklin, V. V.; Kuklina, M. M.; Kisova, N. E.; Maslich, M. A.

    2009-12-01

    The results of annual parasitological monitoring in the coastal area near the Abram-mys (Kola Bay, Barents Sea) are presented. The studies were performed in 2006-2007 and included complex examination of the intermediate hosts (mollusks and crustaceans) and definitive hosts (marine fish and birds) of the helminths. The biodiversity of the parasite fauna, seasonal dynamics, and functioning patterns of the parasite systems were investigated. The basic regularities in parasite circulation were assessed in relation to their life cycle strategies and the ecological features of the intermediate and definitive hosts. The factors affecting the success of parasite circulation in the coastal ecosystems were revealed through analysis of parasite biodiversity and abundance dynamics.

  20. Bottom-up control of macrobenthic communities in a guanotrophic coastal system.

    PubMed

    Signa, Geraldina; Mazzola, Antonio; Costa, Valentina; Vizzini, Salvatrice

    2015-01-01

    Soft bottom macrobenthic communities were studied seasonally in three coastal ponds (Marinello ponds, Italy) at increasing distances from a gull (Larus michahellis) colony to investigate the effect of seabird-induced eutrophication (i.e. guanotrophication) on macrobenthic fauna. We hypothesized that enhanced nutrient concentration and organic load caused by guano input significantly alter the trophic and sedimentological condition of ponds, affecting benthic fauna through a bottom-up control. The influence of a set of environmental features on macrobenthic assemblages was also tested. Overall, the lowest macrobenthic abundances and functional group diversity were found in deeper sites, especially in the pond characterised by severe guanotrophication, where the higher disturbance resulted in a decline in suspension feeders and carnivores in favour of deposit feeders. An increase in opportunistic/tolerant taxa (e.g. chironomid larvae and paraonids) and totally azoic sediments were also found as an effect of the harshest environmental conditions, resulting in a very poor ecological status. We conclude that macrobenthic assemblages of the Marinello coastal system display high spatial variability due to a synergistic effect of trophic status and the geomorphological features of the ponds. The macrobenthic response to guanotrophication, which was a clear decrease in abundance, diversity and trophic functional groups, was associated with the typical response to severe eutrophication, magnified by the geomorphological features.

  1. Mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

    DOEpatents

    Korber, Bette T [Los Alamos, NM; Fischer, William [Los Alamos, NM; Liao, Hua-Xin [Durham, NC; Haynes, Barton F [Durham, NC; Letvin, Norman [Boston, MA; Hahn,; Beatrice, H [Birmingham, AL

    2011-05-31

    The present invention relates to mosaic clade M HIV-1 Env polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  2. Seasonal variation in composition and abundance of harmful dinoflagellates in Yemeni waters, southern Red Sea.

    PubMed

    Alkawri, Abdulsalam

    2016-11-15

    General abundance and species composition of a dinoflagellate community in Yemeni coastal waters of Al Salif (southern Red Sea) were studied with a view to understand the annual variations in particular the toxic species. Dinoflagellates were more abundant among phytoplankton. Thirty five dinoflagellate taxa were identified, among which 12 were reported as potentially toxic species. A significant change in seasonal abundance was recorded with the maximum (2.27∗10 6 cellsl -1 ) in May, and the minimum (2.50∗10 2 cellsl -1 ) recorded in January. Kryptoperidinium foliaceum, which was reported for the first time from the Red Sea, was the most abundant species with a maximum in May 2013 (2.26∗10 6 cellsl -1 ). Spearman's rank correlation analysis indicates that, total harmful dinoflagellate cells, K. foliaceum, Prorocentrum gracile and Prorocentrum micans were significantly correlated with temperature. This study suggests that Yemeni waters should be monitored to investigate harmful species and to identify areas and seasons at higher risk. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Development of Clade-Specific and Broadly Reactive Live Attenuated Influenza Virus Vaccines against Rapidly Evolving H5 Subtype Viruses

    PubMed Central

    Boonnak, Kobporn; Matsuoka, Yumiko; Wang, Weijia; Suguitan, Amorsolo L.; Chen, Zhongying; Paskel, Myeisha; Baz, Mariana; Moore, Ian; Jin, Hong

    2017-01-01

    ABSTRACT We have developed pandemic live attenuated influenza vaccines (pLAIVs) against clade 1 H5N1 viruses on an Ann Arbor cold-adapted (ca) backbone that induced long-term immune memory. In 2015, many human infections caused by a new clade (clade 2.2.1.1) of goose/Guangdong (gs/GD) lineage H5N1 viruses were reported in Egypt, which prompted updating of the H5N1 pLAIV. We explored two strategies to generate suitable pLAIVs. The first approach was to modify the hemagglutinin gene of a highly pathogenic wild-type (wt) clade 2.2.1.1 virus, A/Egypt/N03434/2009 (Egy/09) (H5N1), with its unmodified neuraminidase (NA) gene; this virus was designated Egy/09 ca. The second approach was to select a low-pathogenicity avian influenza H5 virus that elicited antibodies that cross-reacted with a broad range of H5 viruses, including the Egypt H5N1 viruses, and contained a novel NA subtype for humans. We selected the low-pathogenicity A/duck/Hokkaido/69/2000 (H5N3) (dk/Hok/00) virus for this purpose. Both candidate vaccines were attenuated and immunogenic in ferrets, inducing antibodies that neutralized homologous and heterologous H5 viruses with different degrees of cross-reactivity; Egy/09 ca vaccine antisera were more specific for the gs/GD lineage viruses but did not neutralize recent North American isolates (clade 2.3.4.4), whereas antisera from dk/Hok/69 ca-vaccinated ferrets cross-reacted with clade 2.3.4.4 and 2.2.1 viruses but not clade 1 or 2.1 viruses. When vaccinated ferrets were challenged with homologous and heterologous H5 viruses, challenge virus replication was reduced in the respiratory tract. Thus, the two H5 pLAIV candidates are suitable for clinical development to protect humans from infection with different clades of H5 viruses. IMPORTANCE In response to the continuing evolution of H5N1 avian influenza viruses and human infections, new candidate H5 live attenuated vaccines were developed by using two different approaches: one targeted a specific circulating

  4. Development of Clade-Specific and Broadly Reactive Live Attenuated Influenza Virus Vaccines against Rapidly Evolving H5 Subtype Viruses.

    PubMed

    Boonnak, Kobporn; Matsuoka, Yumiko; Wang, Weijia; Suguitan, Amorsolo L; Chen, Zhongying; Paskel, Myeisha; Baz, Mariana; Moore, Ian; Jin, Hong; Subbarao, Kanta

    2017-08-01

    We have developed pandemic live attenuated influenza vaccines (pLAIVs) against clade 1 H5N1 viruses on an Ann Arbor cold-adapted ( ca ) backbone that induced long-term immune memory. In 2015, many human infections caused by a new clade (clade 2.2.1.1) of goose/Guangdong (gs/GD) lineage H5N1 viruses were reported in Egypt, which prompted updating of the H5N1 pLAIV. We explored two strategies to generate suitable pLAIVs. The first approach was to modify the hemagglutinin gene of a highly pathogenic wild-type ( wt ) clade 2.2.1.1 virus, A/Egypt/N03434/2009 (Egy/09) (H5N1), with its unmodified neuraminidase (NA) gene; this virus was designated Egy/09 ca The second approach was to select a low-pathogenicity avian influenza H5 virus that elicited antibodies that cross-reacted with a broad range of H5 viruses, including the Egypt H5N1 viruses, and contained a novel NA subtype for humans. We selected the low-pathogenicity A/duck/Hokkaido/69/2000 (H5N3) (dk/Hok/00) virus for this purpose. Both candidate vaccines were attenuated and immunogenic in ferrets, inducing antibodies that neutralized homologous and heterologous H5 viruses with different degrees of cross-reactivity; Egy/09 ca vaccine antisera were more specific for the gs/GD lineage viruses but did not neutralize recent North American isolates (clade 2.3.4.4), whereas antisera from dk/Hok/69 ca -vaccinated ferrets cross-reacted with clade 2.3.4.4 and 2.2.1 viruses but not clade 1 or 2.1 viruses. When vaccinated ferrets were challenged with homologous and heterologous H5 viruses, challenge virus replication was reduced in the respiratory tract. Thus, the two H5 pLAIV candidates are suitable for clinical development to protect humans from infection with different clades of H5 viruses. IMPORTANCE In response to the continuing evolution of H5N1 avian influenza viruses and human infections, new candidate H5 live attenuated vaccines were developed by using two different approaches: one targeted a specific circulating

  5. Effect of land cover, habitat fragmentation and ant colonies on the distribution and abundance of shrews in southern California

    USGS Publications Warehouse

    Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

    2001-01-01

    Because effects of habitat fragmentation and anthropogenic disturbance on native animals have been relatively little studied in arid areas and in insectivores, we investigated the roles of different land covers, habitat fragmentation and ant colonies on the distribution and abundance of shrews, Notiosorex crawfordi and Sorex ornatus, in southern California.Notiosorex crawfordi was the numerically dominant species (trap-success rate 0·52) occurring in 21 of the 22 study sites in 85% of the 286 pitfall arrays used in this study.Sorex ornatus was captured in 14 of the sites, in 52% of the arrays with a total trap-success rate of 0·2. Neither of the species was found in one of the sites.The population dynamics of the two shrew species were relatively synchronous during the 4–5-year study; the peak densities usually occurred during the spring. Precipitation had a significant positive effect, and maximum temperature a significant negative effect on the trap-success rate of S. ornatus.Occurrence and abundance of shrews varied significantly between sites and years but the size of the landscape or the study site had no effect on the abundance of shrews. The amount of urban edge had no significant effect on the captures of shrews but increased edge allows invasion of the Argentine ants, which had a highly significant negative impact on the abundance of N. crawfordi.At the trap array level, the percentage of coastal sage scrub flora had a significant positive, and the percentage of other flora had a significant negative effect on the abundance of N. crawfordi. The mean canopy height and the abundance of N. crawfordi had a significant positive effect on the occurrence of S. ornatus.Our study suggests that the loss of native coastal sage scrub flora and increasing presence of Argentine ant colonies may significantly effect the distribution and abundance of N. crawfordi. The very low overall population densities of both shrew species in most study sites make both species

  6. Short-term meso-scale variability of mesozooplankton communities in a coastal upwelling system (NW Spain)

    NASA Astrophysics Data System (ADS)

    Roura, Álvaro; Álvarez-Salgado, Xosé A.; González, Ángel F.; Gregori, María; Rosón, Gabriel; Guerra, Ángel

    2013-02-01

    The short-term, meso-scale variability of the mesozooplankton community present in the coastal upwelling system of the Ría de Vigo (NW Spain) has been analysed. Three well-defined communities were identified: coastal, frontal and oceanic, according to their holoplankton-meroplankton ratio, richness, and total abundance. These communities changed from summer to autumn due to a shift from downwelling to upwelling-favourable conditions coupled with taxa dependent changes in life strategies. Relationships between the resemblance matrix of mesozooplankton and the resemblance matrices of meteorologic, hydrographic and community-derived biotic variables were determined with distance-based linear models (DistLM, 18 variables), showing an increasing amount of explained variability of 6%, 16.1% and 54.5%, respectively. A simplified model revealed that the variability found in the resemblance matrix of mesozooplankton was mainly described by the holoplankton-meroplankton ratio, the total abundance, the influence of lunar cycles, the upwelling index and the richness; altogether accounting for 64% of the total variability. The largest variability of the mesozooplankton resemblance matrix (39.6%) is accounted by the holoplankton-meroplankton ratio, a simple index that describes appropriately the coastal-ocean gradient. The communities described herein kept their integrity in the studied upwelling and downwelling episodes in spite of the highly advective environment off the Ría de Vigo, presumably due to behavioural changes in the vertical position of the zooplankton.

  7. Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

    PubMed Central

    Lau, Susanna K P; Wernery, Renate; Wong, Emily Y M; Joseph, Sunitha; Tsang, Alan K L; Patteril, Nissy Annie Georgy; Elizabeth, Shyna K; Chan, Kwok-Hung; Muhammed, Rubeena; Kinne, Jöerg; Yuen, Kwok-Yung; Wernery, Ulrich; Woo, Patrick C Y

    2016-01-01

    Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE. PMID:27999424

  8. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  9. Epiphyte loads on seagrasses and microphytobenthos abundance are not reliable indicators of nutrient availability in oligotrophic coastal ecosystems.

    PubMed

    Fourqurean, James W; Muth, Meredith F; Boyer, Joseph N

    2010-07-01

    Despite marked gradients in nutrient availability that control the abundance and species composition of seagrasses in south Florida, and the importance of nutrient availability in controlling abundance and composition of epiphytes on seagrasses in other locations, we did not find that epiphyte load on the dominant seagrass, Thalassia testudinum, or that the relative contribution of algal epiphytes to the epiphyte community, was positively correlated with nutrient availability in the water column or the sediment in oligotrophic seagrass beds. Further, the abundance of microphytobenthos, as indicated by Chlorophyll-a concentration in the sediments, was not directly correlated with concentrations of nutrients in the sediments. Our results suggest that epiphyte and microphytobenthos abundance are not unambiguous indicators of nutrient availability in relatively pristine seagrass environments, and therefore would make poor candidates for indicators of the status and trends of seagrass ecosystems in relatively low-nutrient environments like the Florida Keys. Copyright 2010 Elsevier Ltd. All rights reserved.

  10. Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

    PubMed Central

    Sonnenschein, Eva C; Nielsen, Kristian F; D'Alvise, Paul; Porsby, Cisse H; Melchiorsen, Jette; Heilmann, Jens; Kalatzis, Panos G; López-Pérez, Mario; Bunk, Boyke; Spröer, Cathrin; Middelboe, Mathias; Gram, Lone

    2017-01-01

    Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99–100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture. PMID:27552638

  11. Complete genome sequence of Campylobacter jejuni strain 12567 a livestock-associated clade representative

    USDA-ARS?s Scientific Manuscript database

    We report the complete genome sequence of the Campylobacter jejuni strain 12567, a member of a C. jejuni livestock-associated clade that expresses glycoconjugates linked to improved gastrointestinal tract persistence....

  12. Coastal Prairie

    USGS Publications Warehouse

    ,

    2000-01-01

    The coastal prairie, located along the coastal plain of southwestern Louisiana and southcentral Texas, is the southernmost tip of the tallgrass prairie ecosystem so prevalent in the Midwest. The coastal prairie ecosystem once covered as much as 3.8 million ha (9 million acres); today, more than 99% of this land has been lost to agriculture, range improvement, and urbanization. The remainder is highly fragmented and severely threatened by invasions of exotic species and urban sprawl. In Louisiana, the former 1 million ha of coastal prairie have now been reduced to about 100 ha. In Texas, only about 100,000 ha of coastal prairie remain intact.

  13. Phytophthora borealis and Phytophthora riparia , new species in Phytophthora ITS Clade 6

    Treesearch

    Everrett Hansen; Paul Reeser; Wendy Sutton

    2012-01-01

    Phytopthora borealis and Phytophthora riparia were identified in recent Phytophthora surveys in forest streams in Oregon, California and Alaska are described as new species in Phytophthora ITS Clade 6. They are similar in growth form and morphology to P. gonapodyides...

  14. Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

    PubMed

    Morais, Camila G; Batista, Thiago M; Kominek, Jacek; Borelli, Beatriz M; Furtado, Carolina; Moreira, Rennan G; Franco, Gloria R; Rosa, Luiz H; Fonseca, César; Hittinger, Chris T; Lachance, Marc-André; Rosa, Carlos A

    2017-10-01

    Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus Spathaspora were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to Candida blackwellae, in a clade that also contains Candida albicans and Candida dubliniensis. Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger C. albicans/Lodderomyces clade. One interpretation is that the genus Spathaspora is, in fact, paraphyletic. In conformity with this view, we propose the novel species Spathaspora boniae sp. nov. to accommodate the isolates. The type strain of Spathaspora boniae sp. nov. is UFMG-CM-Y306 T (=CBS 13262 T ). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.

  15. Does coastal lagoon habitat quality affect fish growth rate and their recruitment? Insights from fishing and acoustic surveys

    NASA Astrophysics Data System (ADS)

    Brehmer, P.; Laugier, T.; Kantoussan, J.; Galgani, F.; Mouillot, D.

    2013-07-01

    Ensuring the sustainability of fish resources necessitates understanding their interaction with coastal habitats, which is becoming ever more challenging in the context of ever increasing anthropogenic pressures. The ability of coastal lagoons, exposed to major sources of disturbance, to provide resources and suitable habitats for growth and survival of juvenile fish is especially important. We analysed three lagoons with different ecological statuses and habitat quality on the basis of their eutrophication and ecotoxicity (Trix test) levels. Fish abundances were sampled using fishing and horizontal beaming acoustic surveys with the same protocols in the same year. The relative abundance of Anguilla anguilla, Dicentrarchus labrax or the Mugilidae group was not an indicator of habitat quality, whereas Atherina boyeri and Sparus aurata appeared to be more sensitive to habitat quality. Fish abundance was higher in the two lagoons with high eutrophication and ecotoxicity levels than in the less impacted lagoon, while fish sizes were significantly higher in the two most severely impacted lagoons. This leads us to suggest low habitat quality may increase fish growth rate (by the mean of a cascading effect), but may reduce lagoon juvenile abundance by increasing larval mortality. Such a hypothesis needs to be further validated using greater investigations which take into account more influences on fish growth and recruitment in such variable environments under complex multi-stressor conditions.

  16. Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

    PubMed

    Carvalho-Sobrinho, Jefferson G; Alverson, William S; Alcantara, Suzana; Queiroz, Luciano P; Mota, Aline C; Baum, David A

    2016-08-01

    Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Influence of Environmental Factors on Vibrio spp. in Coastal Ecosystems.

    PubMed

    Johnson, Crystal N

    2015-06-01

    Various studies have examined the relationships between vibrios and the environmental conditions surrounding them. However, very few reviews have compiled these studies into cohesive points. This may be due to the fact that these studies examine different environmental parameters, use different sampling, detection, and enumeration methodologies, and occur in diverse geographic locations. The current article is one approach to compile these studies into a cohesive work that assesses the importance of environmental determinants on the abundance of vibrios in coastal ecosystems.

  18. Predicting Disturbance-driven Impacts on Ecosystem Services in Coastal Wetlands

    NASA Astrophysics Data System (ADS)

    Rajan, S.; Crawford, P.; Kleinhuizen, A.; Mortazavi, B.; Sobecky, P.

    2017-12-01

    Natural and human-induced disturbances pose significant threats to the health and long-term productivity of Alabama coastal wetlands. As wetlands are a vital state resource, decisions on management, restoration, and remediation require actionable data if socio-economic demands are to be balanced with efforts to sustain these habitats. In 2010, the BP oil spill was a large and severe disturbance that threatened coastal Gulf ecosystem services. The largest marine oil spill to date served to highlight fundamental gaps in our knowledge of oil-induced disturbances and the resiliency and restoration of coastal Alabama wetland functions. To address these gaps, a year-long mesocosm study was conducted to investigate oil-induced effects on (i) plant-microbial interactions, (ii) microbial and plant biodiversity, and, (iii) the contributions of microbial genetic biodiversity to ecosystems services. In this study, Avicennia germinans (black mangrove), a C3 plant that grows from the tropics to warm temperate latitudes, were grown with or without mono- and polyculture mixtures of Spartina alterniflora, a C4 plant. At an interval of 3-months, oil was introduced as a pulse disturbance to achieve a concentration of 4000 ppm. Molecular-based analyses of microbial community biodiversity, genetic diversity, and functional metabolic genes were compared to controls (i.e., no oil disturbance). To assess the oil-induced effects on the nitrogen (N) cycle, measurements of denitrification and N fixation processes were conducted. Our results showed that community diversity and phylogenetic diversity significantly changed and that the oil disturbance contributed to the creation of niches for distinct microbial types. The abundance of N-fixing microbial types increased as the abundance of denitrifying microbial types decreased as a result of the oil disturbance. As denitrification is an ecosystem service that directly contributes to removing nitrate (NO3-) loading to coastal zones, impairment

  19. Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade.

    PubMed

    Lagomarsino, Laura P; Forrestel, Elisabeth J; Muchhala, Nathan; Davis, Charles C

    2017-08-01

    Although specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in the centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  20. Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies

    PubMed Central

    Mullen, Sean P.; Savage, Wesley K.; Wahlberg, Niklas; Willmott, Keith R.

    2011-01-01

    Latitudinal gradients in species richness are among the most well-known biogeographic patterns in nature, and yet there remains much debate and little consensus over the ecological and evolutionary causes of these gradients. Here, we evaluated whether two prominent alternative hypotheses (namely differences in diversification rate or clade age) could account for the latitudinal diversity gradient in one of the most speciose neotropical butterfly genera (Adelpha) and its close relatives. We generated a multilocus phylogeny of a diverse group of butterflies in the containing tribe Limenitidini, which has both temperate and tropical representatives. Our results suggest there is no relationship between clade age and species richness that could account for the diversity gradient, but that instead it could be explained by a significantly higher diversification rate within the predominantly tropical genus Adelpha. An apparent early larval host-plant shift to Rubiaceae and other plant families suggests that the availability of new potential host plants probably contributed to an increase in diversification of Adelpha in the lowland Neotropics. Collectively, our results support the hypothesis that the equatorial peak in species richness observed within Adelpha is the result of increased diversification rate in the last 10–15 Myr rather than a function of clade age, perhaps reflecting adaptive divergence in response to the dramatic host-plant diversity found within neotropical ecosystems. PMID:21106589

  1. Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area.

    PubMed

    Thiele, Stefan; Richter, Michael; Balestra, Cecilia; Glöckner, Frank Oliver; Casotti, Raffaella

    2017-04-01

    The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics. Bacteria and Archaea were mainly represented by marine clades, with only minor contributors from freshwater ones. The community was dominated by Alpha- and Gammaproteobacteria, of which Rhodospirillales, Pelagibacteriales, and Oceanospirilalles were most represented. However, Alteromonadales and Rhodobacterales were the most active, despite their relative lower abundance, suggesting that they are important for overall ecosystem functioning and nutrient cycling. Nitrification and a reversed form of dissimilatory sulfate reduction were the major metabolic processes found in the metatrascriptomes and were mainly associated to Nitrosopumilales and Pelagibacter, respectively. No clear indication of transcripts related to stress induced by heavy metals or organic pollutants was found. In general, despite the high loads of pollutants discharged continuously by the Sarno River, the microbial community did not show marks of stress-induced changes neither structural nor functional, thus suggesting that this river has little or no effect on the planktonic bacterial community of the Gulf of Naples. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Comparative analysis of different survey methods for monitoring fish assemblages in coastal habitats.

    PubMed

    Baker, Duncan G L; Eddy, Tyler D; McIver, Reba; Schmidt, Allison L; Thériault, Marie-Hélène; Boudreau, Monica; Courtenay, Simon C; Lotze, Heike K

    2016-01-01

    Coastal ecosystems are among the most productive yet increasingly threatened marine ecosystems worldwide. Particularly vegetated habitats, such as eelgrass (Zostera marina) beds, play important roles in providing key spawning, nursery and foraging habitats for a wide range of fauna. To properly assess changes in coastal ecosystems and manage these critical habitats, it is essential to develop sound monitoring programs for foundation species and associated assemblages. Several survey methods exist, thus understanding how different methods perform is important for survey selection. We compared two common methods for surveying macrofaunal assemblages: beach seine netting and underwater visual census (UVC). We also tested whether assemblages in shallow nearshore habitats commonly sampled by beach seines are similar to those of nearby eelgrass beds often sampled by UVC. Among five estuaries along the Southern Gulf of St. Lawrence, Canada, our results suggest that the two survey methods yield comparable results for species richness, diversity and evenness, yet beach seines yield significantly higher abundance and different species composition. However, sampling nearshore assemblages does not represent those in eelgrass beds despite considerable overlap and close proximity. These results have important implications for how and where macrofaunal assemblages are monitored in coastal ecosystems. Ideally, multiple survey methods and locations should be combined to complement each other in assessing the entire assemblage and full range of changes in coastal ecosystems, thereby better informing coastal zone management.

  3. Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker.

    PubMed

    Zeng, Wei; Zhang, Limin; Fan, Pengchao; Guo, Jingjing; Peng, Yongzhen

    2018-05-01

    Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A 2 O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10 9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A 2 O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter. Copyright © 2017. Published by Elsevier B.V.

  4. Identification of Cyanobacteria in a Eutrophic Coastal Lagoon on the Southern Baltic Coast

    PubMed Central

    Albrecht, Martin; Pröschold, Thomas; Schumann, Rhena

    2017-01-01

    Cyanobacteria are found worldwide in various habitats. Members of the picocyanobacteria genera Synechococcus and Prochlorococcus dominate in oligotrophic ocean waters. Other picocyanobacteria dominate in eutrophic fresh or brackish waters. Usually, these are morphologically determined as species of the order Chroococcales/clade B2. The phytoplankton of a shallow, eutrophic brackish lagoon was investigated. Phytoplankton was dominated by Aphanothece-like morphospecies year-round for more than 20 years, along a trophy and salinity gradient. A biphasic approach using a culture-independent and a culture-dependent analysis was applied to identify the dominant species genetically. The 16S rRNA gene phylogeny of clone sequences and isolates indicated the dominance of Cyanobium species (order Synechococcales sensu Komárek/clade C1 sensu Shih). This difference between morphologically and genetically based species identifications has consequences for applying the Reynolds functional-groups system, and for validity long-term monitoring data. The literature shows the same pattern as our results: morphologically, Aphanothece-like species are abundant in eutrophic shallow lagoons, and genetically, Cyanobium is found in similar habitats. This discrepancy is found worldwide in the literature on fresh- and brackish-water habitats. Thus, most Aphanothece-like morphospecies may be, genetically, members of Cyanobium. PMID:28611738

  5. Shell alterations in limpets as putative biomarkers for multi-impacted coastal areas.

    PubMed

    Begliomini, Felipe Nincao; Maciel, Daniele Claudino; de Almeida, Sérgio Mendonça; Abessa, Denis Moledo; Maranho, Luciane Alves; Pereira, Camilo Seabra; Yogui, Gilvan Takeshi; Zanardi-Lamardo, Eliete; Castro, Ítalo Braga

    2017-07-01

    During the last years, shell alterations in gastropods have been proposed as tools to be used in monitoring programs. However, no studies were so far performed investigating the relationships among shell parameters and classical biomarkers of damage. The relationship between shell alterations (biometrics, shape and elemental composition) and biomarkers (LPO and DNA strand break) was evaluated in the limpet L. subrugosa sampled along a contamination gradient in a multi-impacted coastal zone from southeastern Brazil. Statistically significant differences were detected among sites under different pollution levels. The occurrence of shell malformations was consistent with environmental levels of several hazardous substances reported for the studied area and related to lipid peroxidation and DNA damage. In addition, considering the low mobility, wide geographic distribution, ease of collection and abundance of limpets in coastal zones, this putative tool may be a cost-effective alternative to traditional biomarkers. Thus, shell alterations in limpets seem to be good proxies for assessing biological adverse effects in multi-impacted coastal zones. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Genome-Wide Comparison of Cowpox Viruses Reveals a New Clade Related to Variola Virus

    PubMed Central

    Kurth, Andreas; Nitsche, Andreas

    2013-01-01

    Zoonotic infections caused by several orthopoxviruses (OPV) like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV) is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages. PMID:24312452

  7. Genome-wide comparison of cowpox viruses reveals a new clade related to Variola virus.

    PubMed

    Dabrowski, Piotr Wojtek; Radonić, Aleksandar; Kurth, Andreas; Nitsche, Andreas

    2013-01-01

    Zoonotic infections caused by several orthopoxviruses (OPV) like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV) is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages.

  8. Global cooling as a driver of diversification in a major marine clade

    NASA Astrophysics Data System (ADS)

    Davis, Katie E.; Hill, Jon; Astrop, Tim I.; Wills, Matthew A.

    2016-10-01

    Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems.

  9. Environmental response to long-term mariculture activities in the Weihai coastal area, China.

    PubMed

    Li, Hongmei; Li, Xiaomin; Li, Qiang; Liu, Ying; Song, Jide; Zhang, Yongyu

    2017-12-01

    The environmental impacts of rapid expansion of mariculture have garnered worldwide attention. China is currently one of the largest countries to engage in this practice. In this study, a representative mariculture zone, the Weihai coastal area in China, was explored to determine the temporal variations in regional nutrients, N/P ratio, dissolved oxygen (DO), pH, chlorophyll a (Chl-a), and cellular abundance of diatoms and dinoflagellates in response to the rapid growth in mariculture activities between 2006 and 2014. The temporal variations in inorganic and organic nitrogen concentrations in the surface water presented significantly increasing trends during August, between 2009 and 2014. A marked increase in the ratios of dinoflagellate to diatom abundance, concurrently with ascending N/P ratios, was also observed during August between 2011 and 2014. In addition, dissolved inorganic nitrogen and phosphate variations revealed the highest concentrations during October and lower levels during May and August, which was attributed in part to the seasonal growth characteristics of kelp cultivated in the study area. Moreover, the nutrient concentrations in Sanggou, Rongcheng, Wulei, and Rushan bays were affected significantly by the various cultured organisms in these bays. The intensive mariculture activity in the Weihai coastal area is likely one of the causes of the negative effects on water quality, such as eutrophication and future ocean acidification. The exploration of effective strategies is quite necessary in the future for keeping good quality of coastal environment and sustainable mariculture development. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Sea-level rise and coastal groundwater inundation and shoaling at select sites in California, USA

    USGS Publications Warehouse

    Hoover, Daniel J.; Odigie, Kingsley; Swarzenski, Peter W.; Barnard, Patrick

    2017-01-01

    Study regionThe study region spans coastal California, USA, and focuses on three primary sites: Arcata, Stinson Beach, and Malibu Lagoon.Study focus1 m and 2 m sea-level rise (SLR) projections were used to assess vulnerability to SLR-driven groundwater emergence and shoaling at select low-lying, coastal sites in California. Separate and combined inundation scenarios for SLR and groundwater emergence were developed using digital elevation models of study site topography and groundwater surfaces constructed from well data or published groundwater level contours.New hydrological insights for the regionSLR impacts are a serious concern in coastal California which has a long (∼1800 km) and populous coastline. Information on the possible importance of SLR-driven groundwater inundation in California is limited. In this study, the potential for SLR-driven groundwater inundation at three sites (Arcata, Stinson Beach, and Malibu Lagoon) was investigated under 1 m and 2 m SLR scenarios. These sites provide insight into the vulnerability of Northern California coastal plains, coastal developments built on beach sand or sand spits, and developed areas around coastal lagoons associated with seasonal streams and berms. Northern California coastal plains with abundant shallow groundwater likely will see significant and widespread groundwater emergence, while impacts along the much drier central and southern California coast may be less severe due to the absence of shallow groundwater in many areas. Vulnerability analysis is hampered by the lack of data on shallow coastal aquifers, which commonly are not studied because they are not suitable for domestic or agricultural use. Shallow saline aquifers may be present in many areas along coastal California, which would dramatically increase vulnerability to SLR-driven groundwater emergence and shoaling. Improved understanding of the extent and response of California coastal aquifers to SLR will help in preparing for mitigation

  11. Detection of bacterial pathogens in clade E head lice collected from Niger's refugees in Algeria.

    PubMed

    Louni, Meriem; Amanzougaghene, Nadia; Mana, Nassima; Fenollar, Florence; Raoult, Didier; Bitam, Idir; Mediannikov, Oleg

    2018-06-15

    Head lice, Pediculus humanus capitis, are obligate blood-sucking parasites. Phylogenetically, they occur in five divergent mitochondrial clades (A, D, B, C and E), each having a particular geographical distribution. Recent studies have revealed that head lice, as is the case of body lice, can act as a vector for louse-borne diseases. Here, we aimed to study the genetic diversity of head lice collected from Niger's refugees (migrant population) arriving in Algeria, northern Africa, and to look for louse-borne pathogens. Comparative head lice samples collected from indigenous population of schoolchildren (non-immigrant) were also analyzed to frame the study. In this study, 37 head lice samples were collected from 31 Nigerien refugees, as well as 45 head lice from 27 schoolchildren. The collection was established in three localities of eastern Algiers, north Algeria. Quantitative real-time PCR screening of pathogens bacteria and the genetic characterisation of the head lice satut were performed. Through amplification and sequencing of the cytb gene, results showed that all head lice of Nigerien refugees 37/82 (45.12%) belonged to clade E with the presence of four new haplotypes, while, of the 45 head lice of schoolchildren, 34/82 lice (41.46%) belonged to clade A and 11/82 (13.41%) belonged to clade B. Our study is the first to report the existence of clade E haplogroup in Nigerien head lice. DNA of Coxiella burnetii was detected in 3/37 (8.10%) of the head lice collected from 3 of the 31 (9.67%) migrant population. We also revealed the presence of Acinetobacter DNA in 20/37 (54.05%) of head lice collected from 25/31 (80.64%) of the Nigerien refugees, and in 25/45 (55.55%) head lice collected from 15/27 (55.55%) schoolchildren. All positive Nigerien-head lice for Acinetobacter spp. were identified as A. baumannii, while positive schoolchildren-head lice were identified as A. johnsonii 15/25 (60%), A. variabilis 8/25 (32%) and A. baumannii 2/25 (8%). Based on these

  12. BIOGEOGRAPHIC DISTRIBUTIONS, ABUNDANCES, AND VULNERABILITIES TO CLIMATE CHANGE OF BRACHYURAN AND LITHODID CRABS FROM THE GULF OF CALIFORNIA TO THE BEAUFORT SEA

    EPA Science Inventory

    As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change we analyzed the biogeographic and abundance patterns of the brachyuran or ‘True’ crabs (n=368) and lithodid or ‘King’ crabs (n=20) that are found...

  13. Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A(H5N1) viruses in ferrets

    USDA-ARS?s Scientific Manuscript database

    Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A (H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, num...

  14. Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4

    PubMed Central

    Lee, Dong-Hun; Bertran, Kateri; Kwon, Jung-Hoon

    2017-01-01

    Novel subtypes of Asian-origin (Goose/Guangdong lineage) H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4, such as H5N2, H5N5, H5N6, and H5N8, have been identified in China since 2008 and have since evolved into four genetically distinct clade 2.3.4.4 groups (A–D). Since 2014, HPAI clade 2.3.4.4 viruses have spread rapidly via migratory wild aquatic birds and have evolved through reassortment with prevailing local low pathogenicity avian influenza viruses. Group A H5N8 viruses and its reassortant viruses caused outbreaks in wide geographic regions (Asia, Europe, and North America) during 2014–2015. Novel reassortant Group B H5N8 viruses caused outbreaks in Asia, Europe, and Africa during 2016–2017. Novel reassortant Group C H5N6 viruses caused outbreaks in Korea and Japan during the 2016–2017 winter season. Group D H5N6 viruses caused outbreaks in China and Vietnam. A wide range of avian species, including wild and domestic waterfowl, domestic poultry, and even zoo birds, seem to be permissive for infection by and/or transmission of clade 2.3.4.4 HPAI viruses. Further, compared to previous H5N1 HPAI viruses, these reassortant viruses show altered pathogenicity in birds. In this review, we discuss the evolution, global spread, and pathogenicity of H5 clade 2.3.4.4 HPAI viruses. PMID:28859267

  15. Application of Coastal Remote Sensing to Rhincodon Typus Habitat Monitoring Northeast of the Yucatán Peninsula

    NASA Astrophysics Data System (ADS)

    Leben, R. R.; Shannon, M. R.

    2013-05-01

    Whale sharks, Rhincodon Typus, congregate annually in the coastal waters northeast of the Yucatán Peninsula from May through mid-September, with peak abundance in occurring between late July and the middle of August. This coincides with seasonal upwelling along the northern Yucatán coast and the eastern margin of the Yucatán shelf. Remote sensing data, including ocean color, sea surface temperature, ocean vector winds, and satellite altimetry, are used to characterize the physical environment supporting this unique coastal ecology, which also has important economic ramifications for the region because of increasing ecotourism activities focused on whale shark aggregations.

  16. Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4

    USDA-ARS?s Scientific Manuscript database

    Novel subtypes of Eurasian-origin (Goose/Guangdong lineage) H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4 such as H5N2, H5N5, H5N6, and H5N8 have been identified in China since 2008 and subsequently evolved into four genetically distinct groups (A – D) of clade 2.3.4.4...

  17. A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers

    PubMed Central

    Gladyshev, Eugene A.; Meselson, Matthew; Arkhipova, Irina R.

    2007-01-01

    Rotifers of class Bdelloidea, a group of aquatic invertebrates in which males and meiosis have never been documented, are also unusual in their lack of multicopy LINE-like and gypsy-like retrotransposons, groups inhabiting the genomes of nearly all other metazoans. Bdelloids do contain numerous DNA transposons, both intact and decayed, and domesticated Penelope-like retroelements Athena, concentrated at telomeric regions. Here we describe two LTR retrotransposons, each found at low copy number in a different bdelloid species, which define a clade different from previously known clades of LTR retrotransposons. Like bdelloid DNA transposons and Athena, these elements have been found preferentially in telomeric regions. Unlike bdelloid DNA transposons, many of which are decayed, the newly described elements, named Vesta and Juno, inhabiting the genomes of Philodina roseola and Adineta vaga, respectively, appear to be intact and to represent recent insertions, possibly from an exogenous source. We describe the retrovirus-like structure of the new elements, containing gag, pol, and env-like open reading frames, and discuss their possible origins, transmission, and behavior in bdelloid genomes. PMID:17129685

  18. A New Clade of African Body and Head Lice Infected by Bartonella quintana and Yersinia pestis-Democratic Republic of the Congo.

    PubMed

    Drali, Rezak; Shako, Jean-Christophe; Davoust, Bernard; Diatta, Georges; Raoult, Didier

    2015-11-01

    The human body louse is known as a vector for the transmission of three serious diseases-specifically, epidemic typhus, trench fever, and relapsing fever caused by Rickettsia prowazekii, Bartonella quintana, and Borrelia recurrentis, respectively-that have killed millions of people. It is also suspected in the transmission of a fourth pathogen, Yersinia pestis, which is the etiologic agent of plague. To date, human lice belonging to the genus Pediculus have been classified into three mitochondrial clades: A, B, and C. Here, we describe a fourth mitochondrial clade, Clade D, comprising head and body lice. Clade D may be a vector of B. quintana and Y. pestis, which is prevalent in a highly plague-endemic area near the Rethy Health District, Orientale Province, Democratic Republic of the Congo. © The American Society of Tropical Medicine and Hygiene.

  19. Taxonomy of the ant genus Proceratium Roger (Hymenoptera, Formicidae) in the Afrotropical region with a revision of the P.arnoldi clade and description of four new species.

    PubMed

    Hita Garcia, Francisco; Hawkes, Peter G; Alpert, Gary D

    2014-01-01

    The taxonomy of the genus Proceratium Roger is updated for the Afrotropical region. We give an overview of the genus in the region, provide an illustrated identification key to the three clades (Proceratiumarnoldi, Proceratiumstictum and Proceratiumtoschii clades) and revise the Proceratiumarnoldi clade. Four new species from the Proceratiumarnoldi clade are described as new: Proceratiumsokoke sp. n. from Kenya, Proceratiumcarri sp. n. from Mozambique, and Proceratiumnilo sp. n. and Proceratiumsali sp. n. from Tanzania. In order to integrate the new species into the existing taxonomic system we present an illustrated identification key to distinguish the seven Afrotropical species of the Proceratiumarnoldi clade. In addition, we provide accounts for all members of the Proceratiumarnoldi clade including detailed descriptions, diagnoses, taxonomic discussions, distribution data and high quality montage images.

  20. A 12-year molecular survey of clinical herpes simplex virus type 2 isolates demonstrates the circulation of clade A and B strains in Germany.

    PubMed

    Schmidt-Chanasit, Jonas; Bialonski, Alexandra; Heinemann, Patrick; Ulrich, Rainer G; Günther, Stephan; Rabenau, Holger F; Doerr, Hans Wilhelm

    2010-07-01

    Recently two different herpes simplex virus type 2 (HSV-2) clades (A and B) were described on DNA sequence data of the glycoprotein E (gE), G (gG) and I (gI) genes. To type the circulating HSV-2 wild-type strains in Germany by a novel approach and to monitor potential changes in the molecular epidemiology between 1997 and 2008. A total of 64 clinical HSV-2 isolates were analyzed by a novel approach using the DNA sequences of the complete open reading frames of glycoprotein B (gB) and gG. Recombination analysis of the gB and gG gene sequences was performed to reveal intragenic recombinants. Based on the phylogenetic analysis of the gB coding DNA sequence 8 of 64 (12%) isolates were classified as clade A strains and 56 of 64 (88%) isolates were classified as clade B strains. Analysis of the gG coding DNA sequence classified 4 (6%) isolates as clade A strains and 60 (94%) isolates as clade B strains. In comparison, the 8 isolates classified as clade A strains using the gB sequence data were classified as clade B strains when using the gG coding DNA sequence, suggesting intergenic recombination events. Intragenic recombination events were not detected. The first molecular survey of clinical HSV-2 isolates from Germany demonstrated the circulation of clade A and B strains and of intergenic recombinants over a period of 12 years. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  1. The potential accumulation of polycyclic aromatic hydrocarbons in phytoplankton and bivalves in Can Gio coastal wetland, Vietnam.

    PubMed

    Thuy, Hoang Thi Thanh; Loan, Tu Thi Cam; Phuong, Trinh Hong

    2018-05-12

    Polycyclic aromatic hydrocarbons (PAHs) are one of the most important classes of anthropogenic persistent organic contaminants in the marine environment. This review discusses a whole range of findings that address various aspects of the bioaccumulation of PAHs in two common marine biota (phytoplankton and bivalves) globally and especially for Can Gio coastal wetland, Vietnam. The published information and collected data on the bioconcentration and accumulation mechanisms of PAHs as well as implications for Can Gio coastal wetland are compiled for phytoplankton and bivalves. PAHs are still released to Can Gio coastal environments from various sources and then transported to coastal environments through various physical processes; they may enter marine food chains and be highly accumulated in phytoplankton and bivalves. Thus, PAHs' bioaccumulation should be considered as one important criterion to assess the water's quality, directly linked to human health due to seafood consumption. Ecologically, Can Gio coastal wetland plays an important role to the South Vietnam key economic zone. However, it is also an area of potential PAHs inputs. With the abundant phytoplankton and bivalves in Can Gio coastal wetland, the PAHs bioaccumulation in these biota is inevitably detected. Thus, further study on the bioavailability of these contaminants is urgently needed in order to mitigate their negative effects and protect the ecosystems.

  2. Coastal sedimentation

    NASA Technical Reports Server (NTRS)

    Schubel, J. R.

    1980-01-01

    Several important coastal sedimentation problems are identified. Application of existing or anticipated remote sensing techniques to examine these problems is considered. Specifically, coastal fine particle sediment systems, floods and hy hurricanes and sedimentation f of coastal systems, routes and rates of sediment transport on continental shelves, and dredging and dredged material disposal are discussed.

  3. Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

    USGS Publications Warehouse

    Garver, K.A.; Troyer, R.M.; Kurath, G.

    2003-01-01

    Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream.

  4. Diel variation of ichthyoplankton recruitment in a wind-dominated temperate coastal lagoon (Argentina)

    NASA Astrophysics Data System (ADS)

    Bruno, Daniel O.; Delpiani, Sergio M.; Acha, Eduardo M.

    2018-05-01

    This study aimed to assess the diel changes of ichthyoplankton occurrence, during a known recruitment period, to a wind-dominated coastal lagoon (Argentina). We collected plankton samples at three sites of the lagoon's inlet area every 3 h during four 24 h cycles in mid austral summer. For each early-life history stage (eggs, yolk sac, preflexion larvae, postflexion larvae and early juveniles), the relationship between the abundance and possible combinations of the time of sampling, the wind effect, the wave period and the tidal state was evaluated by fitting generalized linear mix-effects models (GLMM). The wind effects depending on the time of sampling mainly affected fish abundance in all developmental stages. Overall, the highest abundances were collected at nocturnal hours when low-speed offshore winds blew. In addition, higher abundances of eggs, yolk sac and preflexion larvae were related to the incoming flood tide; whereas higher abundances of postflexion larvae and early juveniles were related to longer wave periods. We argued that the daily variation in the abundance of early-life history stages of fishes is related to the sea-land breeze cycle. Therefore, a conceptual framework of the recruitment process of eggs, larvae and early juveniles of fishes into this estuarine system considering the daily effect of winds is proposed.

  5. Bottom-Up Control of Macrobenthic Communities in a Guanotrophic Coastal System

    PubMed Central

    Signa, Geraldina; Mazzola, Antonio; Costa, Valentina; Vizzini, Salvatrice

    2015-01-01

    Soft bottom macrobenthic communities were studied seasonally in three coastal ponds (Marinello ponds, Italy) at increasing distances from a gull (Larus michahellis) colony to investigate the effect of seabird-induced eutrophication (i.e. guanotrophication) on macrobenthic fauna. We hypothesized that enhanced nutrient concentration and organic load caused by guano input significantly alter the trophic and sedimentological condition of ponds, affecting benthic fauna through a bottom-up control. The influence of a set of environmental features on macrobenthic assemblages was also tested. Overall, the lowest macrobenthic abundances and functional group diversity were found in deeper sites, especially in the pond characterised by severe guanotrophication, where the higher disturbance resulted in a decline in suspension feeders and carnivores in favour of deposit feeders. An increase in opportunistic/tolerant taxa (e.g. chironomid larvae and paraonids) and totally azoic sediments were also found as an effect of the harshest environmental conditions, resulting in a very poor ecological status. We conclude that macrobenthic assemblages of the Marinello coastal system display high spatial variability due to a synergistic effect of trophic status and the geomorphological features of the ponds. The macrobenthic response to guanotrophication, which was a clear decrease in abundance, diversity and trophic functional groups, was associated with the typical response to severe eutrophication, magnified by the geomorphological features. PMID:25679400

  6. Global cooling as a driver of diversification in a major marine clade

    PubMed Central

    Davis, Katie E.; Hill, Jon; Astrop, Tim I.; Wills, Matthew A.

    2016-01-01

    Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems. PMID:27701377

  7. New clades of euthyneuran gastropods (Mollusca) from 28S rRNA sequences.

    PubMed

    Dayrat, B; Tillier, A; Lecointre, G; Tillier, S

    2001-05-01

    Recent morphological and molecular results on phylogeny of euthyneuran gastropods, which include opisthobranchs and pulmonates, have greatly diminished previous supposed resolution of their phylogenetic relationships. In addition to recent morphological results, sequences of the D1 and D2 domains of the 28S rRNA are here analyzed by parsimony for 31 euthyneuran species. The molecular and previous morphological data sets were not congruent according to an ILD test, and morphological and molecular data could not be analyzed simultaneously. Consequently Bremer's Combinable Component Consensus was used to obtain a new tree, with the following supported molecular results: monophyly of a new clade of opisthobranchs including actively swimming Euthyneura, i.e., pelagic Gymnosomata and Thecosomata plus benthic Anaspidea; first molecular confirmation of monophylies of Hygrophila, including Chilina, Acteonoidea, and Sacoglossa, which include both shell-bearing species and slugs; and new confirmation of the monophyly of Stylommatophora. Morphological characters which support the new clades obtained here are discussed. Copyright 2001 Academic Press.

  8. Differential Th17 response induced by the two clades of the pandemic ST258 Klebsiella pneumoniae clonal lineages producing KPC-type carbapenemase

    PubMed Central

    Clemente, Ann Maria; Castronovo, Giuseppe; Antonelli, Alberto; D’Andrea, Marco Maria; Tanturli, Michele; Perissi, Eloisa; Paccosi, Sara; Parenti, Astrid; Cozzolino, Federico; Rossolini, Gian Maria

    2017-01-01

    The spread of KPC-type carbapenemases is mainly attributed to the global dissemination of Klebsiella pneumoniae (KP) strains belonging to the clonal group (CG) 258, including sequence type (ST) 258 and other related STs. Two distinct clades of CG258-KP have evolved, which differ mainly for the composition of their capsular polysaccharides, and recent studies indicate that clade 1 evolved from an ancestor of clade 2 by recombination of a genomic fragment carrying the capsular polysaccharide (cps) locus. In this paper, we investigated the ability of two ST258-KP strains, KKBO-1 and KK207-1, selected as representatives of ST258-KP clade 2 and clade 1, respectively, to activate an adaptive immune response using ex vivo-stimulation of PBMC from normal donors as an experimental model. Our data showed that KKBO-1 (clade 2) induces a Th17 response more efficiently than KK207-1 (clade 1): the percentage of CD4+IL17+ cells and the production of IL-17A were significantly higher in cultures with KKBO-1 compared to cultures with KK207-1. While no differences in the rate of bacterial internalization or in the bacteria-induced expression of CD86 and HLA-DR by monocytes and myeloid dendritic cells were revealed, we found that the two strains significantly differ in inducing the production of cytokines involved in the adaptive immune response, as IL-1β, IL-23 and TNF-α, by antigen-presenting cells, with KKBO-1 being a more efficient inducer than KK207-1. The immune responses elicited by KK207-1 were comparable to those elicited by CIP 52.145, a highly virulent K. pneumoniae reference strain known to escape immune-inflammatory responses. Altogether, present results suggest that CG258-KP of the two clades are capable of inducing a different response of adaptive immunity in the human host. PMID:28586386

  9. A revision of the Dulcamaroid Clade of  Solanum L. (Solanaceae)

    PubMed Central

    Knapp, Sandra

    2013-01-01

    Abstract The Dulcamaroid clade of Solanum contains 45 species of mostly vining or weakly scandent species, including the common circumboreal weed Solanum dulcamara L. The group comprises members of the previously recognised infrageneric groupings sect. Andropedas Rusby, sect. Californisolanum A. Child, sect. Dulcamara (Moench) Dumort., sect. Holophylla (G.Don) Walp., sect. Jasminosolanum (Bitter) Seithe, sect.Lysiphellos (Bitter) Seithe, subsect. Nitidum A.Child and sect. Subdulcamara Dunal. These infrageneric groups are not monophyletic as traditionally recognised, and the complex history of the classification of the dulcamaroid solanums is reviewed. Many of the species in the clade are quite variable morphologically; plants are shrubs, herbaceous vines or woody canopy lianas, and habits can vary between these states in a single locality. Variation in leaf shape and pubescence density and type is also extreme and has lead to the description of many minor morphological variants as distinct species. The flowers of members of the group are generally very showy, and several species (e.g., Solanum crispum Ruiz & Pav., Solanum laxum Spreng., Solanum seaforthianum Andrews) are popular ornamental plants that have occasionally escaped from cultivation and become naturalised. The clade is here divided into five morphologically and geographically delimited species groups to facilitate further study. One new species from southern Ecuador, Solanum agnoston S.Knapp sp. nov., is described here. Full descriptions and synonymies (including designations of lectotypes or neotypes), preliminary conservation assessments, illustrations, distribution maps, and an extensive list of localities are provided for all species. PMID:23794937

  10. Characterizing estuarine plume discharge into the coastal ocean using fatty acid biomarkers and pigment analysis.

    PubMed

    Fischer, Andrew M; Ryan, John P; Levesque, Christian; Welschmeyer, Nicholas

    2014-08-01

    The transformation of estuaries by human activities continues to alter the biogeochemical balance of the coastal ocean. The disruption of this balance can negatively impact the provision of goods and services, including fisheries, commerce and transportation, recreation and esthetic enjoyment. Here we examine a link, between the Elkhorn Slough and the coastal ocean in Monterey Bay, California (USA) using a novel application of fatty acid and pigment analysis. Fatty acid analysis of filtered water samples showed biologically distinct water types between the Elkhorn Slough plume and the receiving waters of the coastal ocean. A remarkable feature of the biological content of the plume entering the coastal ocean was the abundance of bacteria-specific fatty acids, which correlated well with concentrations of colored dissolved organic matter (CDOM). Pigment analysis showed that plume waters contained higher concentrations of diatoms and cryptophytes, while the coastal ocean waters showed higher relative concentrations of dinoflagellates. Bacteria and cryptophytes can provide a source of labile, energy-rich organic matter that may be locally important as a source of food for pelagic and benthic communities. Surface and depth surveys of the plume show that the biogeochemical constituents of the slough waters are injected into the coastal waters and become entrained in the northward flowing, nearshore current of Monterey Bay. Transport of these materials to the northern portion of the bay can fuel a bloom incubator, which exists in this region. This study shows that fatty acid markers can reveal the biogeochemical interactions between estuaries and the coastal ocean and highlights how man-made changes have the potential to influence coastal ecological change. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Techniques for Producing Coastal Land Water Masks from Landsat and Other Multispectral Satellite Data

    NASA Technical Reports Server (NTRS)

    Spruce, Joseph P.; Hall, Callie

    2005-01-01

    Coastal erosion and land loss continue to threaten many areas in the United States. Landsat data has been used to monitor regional coastal change since the 1970s. Many techniques can be used to produce coastal land water masks, including image classification and density slicing of individual bands or of band ratios. Band ratios used in land water detection include several variations of the Normalized Difference Water Index (NDWI). This poster discusses a study that compares land water masks computed from unsupervised Landsat image classification with masks from density-sliced band ratios and from the Landsat TM band 5. The greater New Orleans area is employed in this study, due to its abundance of coastal habitats and its vulnerability to coastal land loss. Image classification produced the best results based on visual comparison to higher resolution satellite and aerial image displays. However, density sliced NDWI imagery from either near infrared (NIR) and blue bands or from NIR and green bands also produced more effective land water masks than imagery from the density-sliced Landsat TM band 5. NDWI based on NIR and green bands is noteworthy because it allows land water masks to be generated from multispectral satellite sensors without a blue band (e.g., ASTER and Landsat MSS). NDWI techniques also have potential for producing land water masks from coarser scaled satellite data, such as MODIS.

  12. Techniques for Producing Coastal Land Water Masks from Landsat and Other Multispectral Satellite Data

    NASA Technical Reports Server (NTRS)

    Spruce, Joe; Hall, Callie

    2005-01-01

    Coastal erosion and land loss continue to threaten many areas in the United States. Landsat data has been used to monitor regional coastal change since the 1970's. Many techniques can be used to produce coastal land water masks, including image classification and density slicing of individual bands or of band ratios. Band ratios used in land water detection include several variations of the Normalized Difference Water Index (NDWI). This poster discusses a study that compares land water masks computed from unsupervised Landsat image classification with masks from density-sliced band ratios and from the Landsat TM band 5. The greater New Orleans area is imployed in this study, due to its abundance of coastal habitats and ist vulnerability to coastal land loss. Image classification produced the best results based on visual comparison to higher resolution satellite and aerial image displays. However, density-sliced NDWI imagery from either near infrared (NIR) and blue bands or from NIR and green bands also produced more effective land water masks than imagery from the density-sliced Landsat TM band 5. NDWI based on NIR and green bands is noteworthy because it allows land water masks to be generated form multispectral satellite sensors without a blue band (e.g., ASTER and Landsat MSS). NDWI techniques also have potential for producing land water masks from coarser scaled satellite data, such as MODIS.

  13. Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale.

    PubMed

    Serafy, Joseph E; Shideler, Geoffrey S; Araújo, Rafael J; Nagelkerken, Ivan

    2015-01-01

    Several studies conducted at the scale of islands, or small sections of continental coastlines, have suggested that mangrove habitats serve to enhance fish abundances on coral reefs, mainly by providing nursery grounds for several ontogenetically-migrating species. However, evidence of such enhancement at a regional scale has not been reported, and recently, some researchers have questioned the mangrove-reef subsidy effect. In the present study, using two different regression approaches, we pursued two questions related to mangrove-reef connectivity at the Caribbean regional scale: (1) Are reef fish abundances limited by mangrove forest area?; and (2) Are mean reef fish abundances proportional to mangrove forest area after taking human population density and latitude into account? Specifically, we tested for Caribbean-wide mangrove forest area effects on the abundances of 12 reef fishes that have been previously characterized as "mangrove-dependent". Analyzed were data from an ongoing, long-term (20-year) citizen-scientist fish monitoring program; coastal human population censuses; and several wetland forest information sources. Quantile regression results supported the notion that mangrove forest area limits the abundance of eight of the 12 fishes examined. Linear mixed-effects regression results, which considered potential human (fishing and habitat degradation) and latitudinal influences, suggested that average reef fish densities of at least six of the 12 focal fishes were directly proportional to mangrove forest area. Recent work questioning the mangrove-reef fish subsidy effect likely reflects a failure to: (1) focus analyses on species that use mangroves as nurseries, (2) consider more than the mean fish abundance response to mangrove forest extent; and/or (3) quantitatively account for potentially confounding human impacts, such as fishing pressure and habitat degradation. Our study is the first to demonstrate at a large regional scale (i.e., the Wider

  14. Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale

    PubMed Central

    Serafy, Joseph E.; Shideler, Geoffrey S.; Araújo, Rafael J.; Nagelkerken, Ivan

    2015-01-01

    Several studies conducted at the scale of islands, or small sections of continental coastlines, have suggested that mangrove habitats serve to enhance fish abundances on coral reefs, mainly by providing nursery grounds for several ontogenetically-migrating species. However, evidence of such enhancement at a regional scale has not been reported, and recently, some researchers have questioned the mangrove-reef subsidy effect. In the present study, using two different regression approaches, we pursued two questions related to mangrove-reef connectivity at the Caribbean regional scale: (1) Are reef fish abundances limited by mangrove forest area?; and (2) Are mean reef fish abundances proportional to mangrove forest area after taking human population density and latitude into account? Specifically, we tested for Caribbean-wide mangrove forest area effects on the abundances of 12 reef fishes that have been previously characterized as “mangrove-dependent”. Analyzed were data from an ongoing, long-term (20-year) citizen-scientist fish monitoring program; coastal human population censuses; and several wetland forest information sources. Quantile regression results supported the notion that mangrove forest area limits the abundance of eight of the 12 fishes examined. Linear mixed-effects regression results, which considered potential human (fishing and habitat degradation) and latitudinal influences, suggested that average reef fish densities of at least six of the 12 focal fishes were directly proportional to mangrove forest area. Recent work questioning the mangrove-reef fish subsidy effect likely reflects a failure to: (1) focus analyses on species that use mangroves as nurseries, (2) consider more than the mean fish abundance response to mangrove forest extent; and/or (3) quantitatively account for potentially confounding human impacts, such as fishing pressure and habitat degradation. Our study is the first to demonstrate at a large regional scale (i.e., the Wider

  15. Neuroimaging abnormalities in clade C HIV are independent of Tat genetic diversity.

    PubMed

    Paul, Robert H; Phillips, Sarah; Hoare, Jacqueline; Laidlaw, David H; Cabeen, Ryan; Olbricht, Gayla R; Su, Yuqing; Stein, Dan J; Engelbrecht, Susan; Seedat, Soraya; Salminen, Lauren E; Baker, Laurie M; Heaps, Jodi; Joska, John

    2017-04-01

    Controversy remains regarding the neurotoxicity of clade C human immunodeficiency virus (HIV-C). When examined in preclinical studies, a cysteine to serine substitution in the C31 dicysteine motif of the HIV-C Tat protein (C31S) results in less severe brain injury compared to other viral clades. By contrast, patient cohort studies identify significant neuropsychological impairment among HIV-C individuals independent of Tat variability. The present study clarified this discrepancy by examining neuroimaging markers of brain integrity among HIV-C individuals with and without the Tat substitution. Thirty-seven HIV-C individuals with the Tat C31S substitution, 109 HIV-C individuals without the Tat substitution (C31C), and 34 HIV- controls underwent 3T structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). Volumes were determined for the caudate, putamen, thalamus, corpus callosum, total gray matter, and total white matter. DTI metrics included fractional anisotropy (FA), radial diffusivity (RD), and axial diffusivity (AD). Tracts of interest included the anterior thalamic radiation (ATR), cingulum bundle (CING), uncinate fasciculus (UNC), and corpus callosum (CC). HIV+ individuals exhibited smaller volumes in subcortical gray matter, total gray matter and total white matter compared to HIV- controls. HIV+ individuals also exhibited DTI abnormalities across multiple tracts compared to HIV- controls. By contrast, neither volumetric nor diffusion indices differed significantly between the Tat C31S and C31C groups. Tat C31S status is not a sufficient biomarker of HIV-related brain integrity in patient populations. Clinical attention directed at brain health is warranted for all HIV+ individuals, independent of Tat C31S or clade C status.

  16. National Coastal Geology Program: a plan of geologic research on coastal erosion, coastal wetlands, polluted sediments, and coastal hard-mineral resources

    USGS Publications Warehouse

    ,

    1990-01-01

    More than 50 percent of the U.S. population currently live within 50 miles of an ocean, Great Lake, or major estuary. According to forecasts, the concentration of people along our coastlines will continue to increase into the 21st century. In addition to residential and commercial buildings and facilities worth tens of billions of dollars, the coasts and associated wetlands are natural resources of tremendous value, with estimates in excess of $13 billion per year for commercial and recreational fisheries alone. Human activities and natural processes are stressing the coastal environment. * Each of the coastal states and island territories is suffering problems related to coastal erosion. * Deterioration of wetlands is widespread and of great public concern. * Pollutants carried by rivers or runoff are discharged directly into coastal waters and accumulate in the sediments on the sea floor, in some areas causing damage to living resources and presenting a threat to public health. * Onshore sources for hard-mineral resources, such as sand and gravel used for construction purposes, are becoming increasingly difficult to find. New sources are being sought in coastal waters. Coastal issues will become even more important into the next century if sea level is significantly influenced by climate change and other factors.

  17. Effects of stream-adjacent logging in fishless headwaters on downstream coastal cutthroat trout

    USGS Publications Warehouse

    Bateman, Douglas S.; Sloat, Matthew R.; Gresswell, Robert E.; Berger, Aaron M.; Hockman-Wert, David; Leer, David W.; Skaugset, Arne E.

    2016-01-01

    To investigate effects of headwater logging on downstream coastal cutthroat trout (Oncorhynchus clarkii clarkii) populations, we monitored stream habitat and biotic indicators including biomass, abundance, growth, movement, and survival over 8 years using a paired-watershed approach. Reference and logged catchments were located on private industrial forestland on ∼60-year harvest rotation. Five clearcuts (14% of the logged catchment area) were adjacent to fishless portions of the headwater streams, and contemporary regulations did not require riparian forest buffers in the treatment catchment. Logging did not have significant negative effects on downstream coastal cutthroat trout populations for the duration of the sample period. Indeed, the only statistically significant response of fish populations following logging in fishless headwaters was an increase in late-summer biomass (g·m−2) of age-1+ coastal cutthroat trout in tributaries. Ultimately, the ability to make broad generalizations concerning effects of timber harvest is difficult because response to disturbance (anthropogenically influenced or not) in aquatic systems is complex and context-dependent, but our findings provide one example of environmentally compatible commercial logging in a regenerated forest setting.

  18. Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

    PubMed

    Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

    2018-04-03

    AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

  19. What was natural in the coastal oceans?

    PubMed Central

    Jackson, Jeremy B. C.

    2001-01-01

    Humans transformed Western Atlantic coastal marine ecosystems before modern ecological investigations began. Paleoecological, archeological, and historical reconstructions demonstrate incredible losses of large vertebrates and oysters from the entire Atlantic coast. Untold millions of large fishes, sharks, sea turtles, and manatees were removed from the Caribbean in the 17th to 19th centuries. Recent collapses of reef corals and seagrasses are due ultimately to losses of these large consumers as much as to more recent changes in climate, eutrophication, or outbreaks of disease. Overfishing in the 19th century reduced vast beds of oysters in Chesapeake Bay and other estuaries to a few percent of pristine abundances and promoted eutrophication. Mechanized harvesting of bottom fishes like cod set off a series of trophic cascades that eliminated kelp forests and then brought them back again as fishers fished their way down food webs to small invertebrates. Lastly, but most pervasively, mechanized harvesting of the entire continental shelf decimated large, long-lived fishes and destroyed three-dimensional habitats built up by sessile corals, bryozoans, and sponges. The universal pattern of losses demonstrates that no coastal ecosystem is pristine and few wild fisheries are sustainable along the entire Western Atlantic coast. Reconstructions of ecosystems lost only a century or two ago demonstrate attainable goals of establishing large and effective marine reserves if society is willing to pay the costs. Historical reconstructions provide a new scientific framework for manipulative experiments at the ecosystem scale to explore the feasibility and benefits of protection of our living coastal resources. PMID:11344287

  20. Taxonomy of the ant genus Proceratium Roger (Hymenoptera, Formicidae) in the Afrotropical region with a revision of the P. arnoldi clade and description of four new species

    PubMed Central

    Hita Garcia, Francisco; Hawkes, Peter G.; Alpert, Gary D.

    2014-01-01

    Abstract The taxonomy of the genus Proceratium Roger is updated for the Afrotropical region. We give an overview of the genus in the region, provide an illustrated identification key to the three clades (Proceratium arnoldi, Proceratium stictum and Proceratium toschii clades) and revise the Proceratium arnoldi clade. Four new species from the Proceratium arnoldi clade are described as new: Proceratium sokoke sp. n. from Kenya, Proceratium carri sp. n. from Mozambique, and Proceratium nilo sp. n. and Proceratium sali sp. n. from Tanzania. In order to integrate the new species into the existing taxonomic system we present an illustrated identification key to distinguish the seven Afrotropical species of the Proceratium arnoldi clade. In addition, we provide accounts for all members of the Proceratium arnoldi clade including detailed descriptions, diagnoses, taxonomic discussions, distribution data and high quality montage images. PMID:25349516

  1. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family.

    PubMed

    Alnajar, Seema; Gupta, Radhey S

    2017-10-01

    The family Enterobacteriaceae harbors many important pathogens, however it has proven difficult to reliably distinguish different members of this family or discern their interrelationships. To understand the interrelationships among the Enterobacteriaceae species, we have constructed two comprehensive phylogenetic trees for 78 genome-sequenced Enterobacteriaceae species based on 2487 core genome proteins, and another set of 118 conserved proteins. The genome sequences of Enterobacteriaceae species were also analyzed for genetic relatedness based on average amino acid identity and 16S rRNA sequence similarity. In parallel, comparative genomic studies on protein sequences from the Enterobacteriaceae have identified 88 molecular markers in the form of conserved signature indels (CSIs) that are uniquely shared by specific members of the family. All of these multiple lines of investigations provide consistent evidence that most of the species/genera within the family can be assigned to 6 different subfamily level clades which are designated as the "Escherichia clade", "Klebsiella clade", "Enterobacter clade", "Kosakonia clade", "Cronobacter clade" and "Cedecea clade". The members of the six described clades, in addition to their distinct branching in phylogenetic trees, can now be reliably demarcated in molecular terms on the basis of multiple identified CSIs that are exclusively shared by the group members. Several additional CSIs identified in this work that are either specific for individual genera (viz. Kosakonia, Kluyvera and Escherichia-Shigella), or are present at various taxonomic depths, offer information regarding the interrelationships among the different clades. The described molecular markers provide novel means for diagnostic as well as genetic and biochemical studies on the Enterobacteriaceae species and for resolving the polyphyly of its several genera viz. Escherichia, Enterobacter and Kluyvera. On the bases of our results, we are proposing the

  2. Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013

    PubMed Central

    Balish, Amanda; Hoang, Anh Nguyen; Gustin, Kortney M.; Nhung, Pham Thi; Jones, Joyce; Thu, Ngoc Nguyen; Davis, William; Ngoc, Thao Nguyen Thi; Jang, Yunho; Sleeman, Katrina; Villanueva, Julie; Kile, James; Gubareva, Larisa V.; Lindstrom, Stephen; Tumpey, Terrence M.; Davis, C. Todd; Long, Nguyen Thanh

    2015-01-01

    Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses. PMID:26244768

  3. Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.

    PubMed

    Straub, Shannon C K; Moore, Michael J; Soltis, Pamela S; Soltis, Douglas E; Liston, Aaron; Livshultz, Tatyana

    2014-11-01

    Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the

  4. Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade

    PubMed Central

    Xi, Zhenxiang; Peterson, Kylee; Rushworth, Catherine; Beaulieu, Jeremy; Davis, Charles C.

    2016-01-01

    The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions. PMID:27684711

  5. Extended Shared Socioeconomic Pathways for Coastal Impact Assessment: Spatial Coastal Population Scenarios

    NASA Astrophysics Data System (ADS)

    Merkens, Jan-Ludolf; Reimann, Lena; Hinkel, Jochen; Vafeidis, Athanasios T.

    2016-04-01

    This work extends the Shared Socioeconomic Pathways (SSPs) by developing spatial projections of global coastal population distribution for the five basic SSPs. Based on a series of coastal migration drivers, which were identified from existing literature, we develop coastal narratives for the five basic SSPs (SSP1-5). These narratives account for differences in coastal versus inland population development in urban and rural areas. To spatially distribute population we use the International Institute for Applied Systems Analysis (IIASA) national population and urbanisation projections and employ country-specific growth rates which differ for coastal and inland as well as for urban and rural regions. These rates are derived from spatial analysis of historical population data. We then adjust these rates for each SSP based on the coastal narratives. The resulting global population grids depict the projected distribution of coastal population for each SSP, until the end of the 21st century, at a spatial resolution of 30 arc seconds. These grids exhibit a three- to four-fold increase in coastal population compared to the basic SSPs. Across all SSPs, except for SSP3, coastal population peaks by the middle of the 21st century and declines afterwards. In SSP3 the coastal population grows continuously until 2100. Compared to the base year 2000 the coastal population increases considerably in all SSPs. The extended SSPs are intended to be utilised in Impact, Adaptation and Vulnerability (IAV) assessments as they allow for improved analysis of exposure to sea-level rise and coastal flooding under different physical and socioeconomic scenarios.

  6. Isotope geochemistry and fluxes of carbon and organic matter in tropical small mountainous river systems and adjacent coastal waters of the Caribbean

    USGS Publications Warehouse

    Moyer, Ryan; Bauer, James; Grottoli, Andrea

    2012-01-01

    Recent studies have shown that small mountainous rivers (SMRs) may act as sources of aged and/or refractory carbon (C) to the coastal ocean, which may increase organic C burial at sea and subsidize coastal food webs and heterotrophy. However, the characteristics and spatial and temporal variability of C and organic matter (OM) exported from tropical SMR systems remain poorly constrained. To address this, the abundance and isotopic character (δ13C and Δ14C) of the three major C pools were measured in two Puerto Rico SMRs with catchments dominated by different land uses (agricultural vs. non-agricultural recovering forest). The abundance and character of C pools in associated estuaries and adjacent coastal waters were also examined. Riverine dissolved and particulate organic C (DOC and POC, respectively) concentrations were highly variable with respect to land use and sampling month, while dissolved inorganic C (DIC) was significantly higher at all times in the agricultural catchment. In both systems, riverine DOC and POC ranged from modern to highly aged (2,340 years before present), while DIC was always modern. The agricultural river and irrigation canals contained very old DOC (1,184 and 2,340 years before present, respectively), which is consistent with findings in temperate SMRs and indicates that these tropical SMRs provide a source of aged DOC to the ocean. During months of high river discharge, OM in estuarine and coastal waters had C isotope signatures reflective of direct terrestrial input, indicating that relatively unaltered OM is transported to the coastal ocean at these times. This is also consistent with findings in temperate SMRs and indicates that C transported to the coastal ocean by SMRs may differ from that of larger rivers because it is exported from smaller catchments that have steeper terrains and fewer land-use types.

  7. Natural abundances of carbon isotopes in acetate from a coastal marine sediment

    NASA Technical Reports Server (NTRS)

    Blair, N. E.; Martens, C. S.; Des Marais, D. J.

    1987-01-01

    Measurements of the natural abundances of carbon isotopes were made in acetate samples isolated from the anoxic marine sediment of Cape Lookout Bight, North Carolina. The typical value of the total acetate carbon isotope ratio (delta 13C) was -16.1 +/- 0.2 per mil. The methyl and carboxyl groups were determined to be -26.4 +/- 0.3 and -6.0 +/- 0.3 per mil, respectively, for one sample. The isotopic composition of the acetate is thought to have resulted from isotopic discriminations that occurred during the cycling of that molecule. Measurements of this type, which have not been made previously in the natural environment, may provide information about the dominant microbial pathways in anoxic sediments as well as the processes that influence the carbon isotopic composition of biogenic methane from many sources.

  8. Sampling little fish in big rivers: Larval fish detection probabilities in two Lake Erie tributaries and implications for sampling effort and abundance indices

    USGS Publications Warehouse

    Pritt, Jeremy J.; DuFour, Mark R.; Mayer, Christine M.; Roseman, Edward F.; DeBruyne, Robin L.

    2014-01-01

    Larval fish are frequently sampled in coastal tributaries to determine factors affecting recruitment, evaluate spawning success, and estimate production from spawning habitats. Imperfect detection of larvae is common, because larval fish are small and unevenly distributed in space and time, and coastal tributaries are often large and heterogeneous. We estimated detection probabilities of larval fish from several taxa in the Maumee and Detroit rivers, the two largest tributaries of Lake Erie. We then demonstrated how accounting for imperfect detection influenced (1) the probability of observing taxa as present relative to sampling effort and (2) abundance indices for larval fish of two Detroit River species. We found that detection probabilities ranged from 0.09 to 0.91 but were always less than 1.0, indicating that imperfect detection is common among taxa and between systems. In general, taxa with high fecundities, small larval length at hatching, and no nesting behaviors had the highest detection probabilities. Also, detection probabilities were higher in the Maumee River than in the Detroit River. Accounting for imperfect detection produced up to fourfold increases in abundance indices for Lake Whitefish Coregonus clupeaformis and Gizzard Shad Dorosoma cepedianum. The effect of accounting for imperfect detection in abundance indices was greatest during periods of low abundance for both species. Detection information can be used to determine the appropriate level of sampling effort for larval fishes and may improve management and conservation decisions based on larval fish data.

  9. The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.

    PubMed

    Mustafa, Ghada A; Abd-Elgawad, Amr; Ouf, Amged; Siam, Rania

    2016-07-01

    The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Facilitation influences patterns of perennial species abundance and richness in a subtropical dune system.

    PubMed

    Dalotto, Cecilia E S; Sühs, Rafael B; Dechoum, Michele S; Pugnaire, Francisco I; Peroni, Nivaldo; Castellani, Tânia T

    2018-04-01

    Positive interactions in plant communities are under-reported in subtropical systems most likely because they are not identified as stressful environments. However, environmental factors or disturbance can limit plant growth in any system and lead to stressful conditions. For instance, salinity and low nutrient and water availability generate a gradient of stressful conditions in coastal systems depending on distance to shore. In a tropical coastal system in SE Brazil, we aimed to assess whether Guapira opposita , a shrub common in restinga environments, acted as nurse involved in ecological succession and which factors influenced its facilitation process. We sampled perennial species above 10 cm in height under the canopy of 35 G. opposita individuals and in neighbouring open areas. Shrub height, canopy area and distance to freshwater bodies were measured in the field, and distance to the ocean was obtained from aerial images. In addition, we measured the distance to the closest forest patch as a potential source of seeds. Plant abundance and species richness were higher under the canopy of G. opposita than in open areas. Facilitation by G. opposita was mainly determined by shrub height, which had a positive relationship with woody and bromeliads abundance and species richness while there was no relationship with the other factors. Overall, our data evidence that tropical environments may be highly stressful for plants and that nurse species play a key role in the regeneration of restinga environments, where their presence is critical to maintain ecosystem diversity and function.

  11. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

    PubMed

    Lemay, Matthew A; Russello, Michael A

    2014-11-04

    Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

  12. Towards Defining the Ecological Niches of Novel Coastal Gulf of Mexico Bacterial Isolates

    NASA Astrophysics Data System (ADS)

    Henson, M. W.; Thrash, C.; Nall, E.

    2016-02-01

    The study of microbial contributions to biogeochemistry is critical to understanding the cycles of fundamental compounds and gain predictive capabilities in a changing environment. Such study requires observation of microbial communities and genetics in nature, coupled with experimental testing of hypotheses both in situ and in laboratory settings. This study combines dilution-to-extinction based high-throughput culturing (HTC) with cultivation-independent and geochemical measurements to define potential ecological niches of novel bacterial isolates from the coastal northern Gulf of Mexico (cnGOM). Here we report findings from the first of a three-year project. In total, 43 cultures from seven HTC experiments were capable of being repeatedly transferred. Sanger sequencing of the 16S rRNA gene identified these isolates as belonging to the phyla Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. Eight are being genome sequenced, with two selected for further physiological characterization due to their phylogenic novelty and potential ecological significance. Strain LSUCC101 likely represents a novel family of Gammaproteobacteria (best blast hit to a cultured representative showed 91% sequence identity) and strain LSUCC96 belongs to the OM252 clade, with the Hawaiian isolate HIMB30 as its closest relative. Both are small (0.3-0.5 µm) cocci. The environmental importance of both LSUCC101 and LSUCC96 was illustrated by their presence within the top 30 OTU0.03 of cnGOM 16S rRNA gene datasets as well as within clone libraries from coastal regions around the world. Ongoing work is determining growth efficiencies, substrate utilization profiles, and metabolic potential to elucidate the roles of these organisms in the cnGOM. Comparative genomics will examine the evolutionary divergence of these organisms from their closest neighbors, and metagenomic recruitment to genomes will help identify strain-based variation from different coastal regions.

  13. CRABS IN CRISIS:BIOGEOGRAPHIC DISTRIBUTIONS, ABUNDANCES, AND VULNERABILITIES TO CLIMATE CHANGE OF BRACHYURAN AND LITHODID CRABS FROM THE GULF OF CALIFORNIA TO THE BEAUFORT SEA

    EPA Science Inventory

    To predict the relative vulnerability of near-coastal species to climate change we analyzed the biogeographic and abundance patterns of the brachyuran or ‘True’ crabs (n=368) and lithodid or ‘King’ crabs (n=20) that are found in the twelve MEOW (“Mar...

  14. Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability

    PubMed Central

    McKechnie, Iain; Lepofsky, Dana; Moss, Madonna L.; Butler, Virginia L.; Orchard, Trevor J.; Coupland, Gary; Foster, Fredrick; Caldwell, Megan; Lertzman, Ken

    2014-01-01

    Pacific herring (Clupea pallasii), a foundation of coastal social-ecological systems, is in decline throughout much of its range. We assembled data on fish bones from 171 archaeological sites from Alaska, British Columbia, and Washington to provide proxy measures of past herring distribution and abundance. The dataset represents 435,777 fish bones, dating throughout the Holocene, but primarily to the last 2,500 y. Herring is the single-most ubiquitous fish taxon (99% ubiquity) and among the two most abundant taxa in 80% of individual assemblages. Herring bones are archaeologically abundant in all regions, but are superabundant in the northern Salish Sea and southwestern Vancouver Island areas. Analyses of temporal variability in 50 well-sampled sites reveals that herring exhibits consistently high abundance (>20% of fish bones) and consistently low variance (<10%) within the majority of sites (88% and 96%, respectively). We pose three alternative hypotheses to account for the disjunction between modern and archaeological herring populations. We reject the first hypothesis that the archaeological data overestimate past abundance and underestimate past variability. We are unable to distinguish between the second two hypotheses, which both assert that the archaeological data reflect a higher mean abundance of herring in the past, but differ in whether variability was similar to or less than that observed recently. In either case, sufficient herring was consistently available to meet the needs of harvesters, even if variability is damped in the archaeological record. These results provide baseline information prior to herring depletion and can inform modern management. PMID:24550468

  15. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    PubMed Central

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  16. Factors associated with plant species richness in a coastal tall-grass prairie

    USGS Publications Warehouse

    Grace, James B.; Allain, Larry K.; Allen, Charles

    2000-01-01

    In this study we examine the factors associated with variations in species richness within a remnant tall-grass prairie in order to gain insight into the relative importance of controlling variables. The study area was a small, isolated prairie surrounded by wetlands and located within the coastal prairie region, which occurs along the northwestern Gulf of Mexico coastal plain. Samples were taken along three transects that spanned the prairie. Parameters measured included micro-elevation, soil characteristics, indications of recent disturbance, above-ground biomass (including litter), light penetration through the plant canopy, and species richness. Species richness was found to correlate with micro-elevation, certain soil parameters, and light penetration through the canopy, but not with above-ground biomass. Structural equation analysis was used to assess the direct and indirect effects of micro-elevation, soil properties, disturbance, and indicators of plant abundance on species richness. The results of this analysis showed that observed variations in species richness were primarily associated with variations in environmental effects (from soil and microtopography) and were largely unrelated to variations in measures of plant abundance (biomass and light penetration). These findings suggest that observed variations in species richness in this system primarily resulted from environmental effects on the species pool. These results fit with a growing body of information that suggests that environmental effects on species richness are of widespread importance.

  17. Hydrocarbon Degradation Pathways used by Coastal Sediment Microbial Communities exposed to Crude Oil

    NASA Astrophysics Data System (ADS)

    Spaulding-Astudillo, F.; Sharrar, A.; Orcutt, B.

    2016-02-01

    The site-specific microbial community response to crude oil exposure in marine environments is not well described. Moreover, the abundance of genes implicated in long-chain alkane (LCA) and polycyclic aromatic hydrocarbon (PAH) degradation are not well understood. Coastal sediments from the Beaufort Sea, Gulf of Alaska, and Portland Harbor were treated with crude oil and incubated aerobically. Deep-sea sediments from the Gulf of Mexico were treated with the same crude oil and anaerobically incubated in situ for five months before recovery. Cycloclasticus, a known hydrocarbon-degrader, was abundant in all oiled, aerobic samples regardless of temperature, demonstrating a generalist oil-response strategy. Other hydrocarbon degrading bacteria showed differential response to either site or temperature. Primers for alkB, assA, bssA, and ncr, catabolic gene markers for aerobic LCA degradation, anaerobic LCA degradation, anaerobic LCA & PAH degradation, and anaerobic PAH degradation, respectively, were found in literature and tested on DNA extracts in a QPCR-based assay. Gene abundance was site and condition variable.

  18. 75 FR 44938 - Atlantic Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark Fishery

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-30

    ... Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark Fishery AGENCY: National... moratorium on fishing for Atlantic coastal sharks in the State waters of New Jersey. NMFS canceled the moratorium, as required by the Atlantic Coastal Fisheries Cooperative Management Act (Atlantic Coastal Act...

  19. An invasive foundation species enhances multifunctionality in a coastal ecosystem.

    PubMed

    Ramus, Aaron P; Silliman, Brian R; Thomsen, Mads S; Long, Zachary T

    2017-08-08

    While invasive species often threaten biodiversity and human well-being, their potential to enhance functioning by offsetting the loss of native habitat has rarely been considered. We manipulated the abundance of the nonnative, habitat-forming seaweed Gracilaria vermiculophylla in large plots (25 m 2 ) on southeastern US intertidal landscapes to assess impacts on multiple ecosystem functions underlying coastal ecosystem services. We document that in the absence of native habitat formers, this invasion has an overall positive, density-dependent impact across a diverse set of ecosystem processes (e.g., abundance and richness of nursery taxa, flow attenuation). Manipulation of invader abundance revealed both thresholds and saturations in the provisioning of ecosystem functions. Taken together, these findings call into question the focus of traditional invasion research and management that assumes negative effects of nonnatives, and emphasize the need to consider context-dependence and integrative measurements when assessing the impact of an invader, including density dependence, multifunctionality, and the status of native habitat formers. This work supports discussion of the idea that where native foundation species have been lost, invasive habitat formers may be considered as sources of valuable ecosystem functions.

  20. The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

    PubMed Central

    Yang, Guan-Dong; Agapow, Paul-Michael

    2017-01-01

    The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors. PMID:28644846

  1. Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem

    PubMed Central

    Silbiger, Nyssa J.; Bernatchez, Genevieve; Sorte, Cascade J.B.

    2018-01-01

    Predicting the impacts of ocean acidification in coastal habitats is complicated by bio-physical feedbacks between organisms and carbonate chemistry. Daily changes in pH and other carbonate parameters in coastal ecosystems, associated with processes such as photosynthesis and respiration, often greatly exceed global mean predicted changes over the next century. We assessed the strength of these feedbacks under projected elevated CO2 levels by conducting a field experiment in 10 macrophyte-dominated tide pools on the coast of California, USA. We evaluated changes in carbonate parameters over time and found that under ambient conditions, daytime changes in pH, pCO2, net ecosystem calcification (NEC), and O2 concentrations were strongly related to rates of net community production (NCP). CO2 was added to pools during daytime low tides, which should have reduced pH and enhanced pCO2. However, photosynthesis rapidly reduced pCO2 and increased pH, so effects of CO2 addition were not apparent unless we accounted for seaweed and surfgrass abundances. In the absence of macrophytes, CO2 addition caused pH to decline by ∼0.6 units and pCO2 to increase by ∼487 µatm over 6 hr during the daytime low tide. As macrophyte abundances increased, the impacts of CO2 addition declined because more CO2 was absorbed due to photosynthesis. Effects of CO2addition were, therefore, modified by feedbacks between NCP, pH, pCO2, and NEC. Our results underscore the potential importance of coastal macrophytes in ameliorating impacts of ocean acidification. PMID:29761055

  2. Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem.

    PubMed

    Bracken, Matthew E S; Silbiger, Nyssa J; Bernatchez, Genevieve; Sorte, Cascade J B

    2018-01-01

    Predicting the impacts of ocean acidification in coastal habitats is complicated by bio-physical feedbacks between organisms and carbonate chemistry. Daily changes in pH and other carbonate parameters in coastal ecosystems, associated with processes such as photosynthesis and respiration, often greatly exceed global mean predicted changes over the next century. We assessed the strength of these feedbacks under projected elevated CO 2 levels by conducting a field experiment in 10 macrophyte-dominated tide pools on the coast of California, USA. We evaluated changes in carbonate parameters over time and found that under ambient conditions, daytime changes in pH, p CO 2 , net ecosystem calcification ( NEC ), and O 2 concentrations were strongly related to rates of net community production ( NCP ). CO 2 was added to pools during daytime low tides, which should have reduced pH and enhanced p CO 2 . However, photosynthesis rapidly reduced p CO 2 and increased pH, so effects of CO 2 addition were not apparent unless we accounted for seaweed and surfgrass abundances. In the absence of macrophytes, CO 2 addition caused pH to decline by ∼0.6 units and p CO 2 to increase by ∼487 µatm over 6 hr during the daytime low tide. As macrophyte abundances increased, the impacts of CO 2 addition declined because more CO 2 was absorbed due to photosynthesis. Effects of CO 2 addition were, therefore, modified by feedbacks between NCP , pH, p CO 2 , and NEC . Our results underscore the potential importance of coastal macrophytes in ameliorating impacts of ocean acidification.

  3. 75 FR 9158 - Atlantic Coastal Fisheries Cooperative Management Act Provisions; Coastal Sharks Fishery

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-01

    ... Coastal Fisheries Cooperative Management Act Provisions; Coastal Sharks Fishery AGENCY: National Marine... Commission's Interstate Fishery Management Plan (ISFMP) for Coastal Sharks. Subsequently, the Commission...-compliance review under the provisions of the Atlantic Coastal Fisheries Cooperative Management Act (Atlantic...

  4. Influence of river discharge on abundance and dissemination of heterotrophic, indicator and pathogenic bacteria along the East Coast of India.

    PubMed

    Prasad, V R; Srinivas, T N R; Sarma, V V S S

    2015-06-15

    In order to examine the influence of discharge from different rivers from peninsular India and urban sewage on intensity and dissemination of heterotrophic, indicator and pathogenic bacteria, a study was carried out during peak discharge period along coastal Bay of Bengal. The coastal Bay received freshwater inputs from the river Ganges while Godavari and Krishna contributed to the south. Contrasting difference in salinity, temperature, nutrients and organic matter was observed between north and south east coast of India. The highest heterotrophic, indicator and pathogenic bacterial abundance was observed in the central coastal Bay that received urban sewage from the major city. Intensity and dissemination of heterotrophic, indicator and pathogenic bacteria displayed linear relation with magnitude of discharge. The coliform load was observed up to 100km from the coast suggesting that marine waters were polluted during the monsoon season and its impact on the ecosystem needs further studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. The coastal use structure within the coastal system. A sustainable development-consistent approach

    NASA Astrophysics Data System (ADS)

    Vallega, A.

    1996-01-01

    To contribute to the development of methodological approaches to coastal area management consistent with the sustainable development concept and guidelines provided by UNCED Agenda 21, Chapter 17, first the classifications of coastal uses provided by literature and those adopted by coastal management programmes are presented and discussed. Moving from this basis and reasoning in terms of general system-sustained approach the following concepts and methodological issues are considered: a goal-oriented concept of coastal use; the sustainable development-grounded coastal use framework and the role of discriminants through which it is conceived and described; the relationships between coastal uses; in particular, conflicting relationships focusing attention on conflicts between decision-making centres, as well as users, motivations and tractability of uses; the relationships between coastal uses and the ecosystem; the basic options for sustainability-consistent coastal use development.

  6. BIOGEOGRAPHIC DISTRIBUTIONS, ABUNDANCES, AND VULNERABILITIES TO CLIMATE CHANGE OF BRACHYURAN AND LITHODID CRABS FROM THE GULF OF CALIFORNIA TO THE BEAUFORT SEA - 9-19-2014

    EPA Science Inventory

    As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change we analyzed the biogeographic and abundance patterns of the brachyuran or ‘True’ crabs (n=368) and lithodid or ‘King’ crabs (n=20) that are found...

  7. Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015

    PubMed Central

    Jang, Yunho; Nguyen, Tho D.; Jones, Joyce; Shepard, Samuel S.; Yang, Hua; Gerloff, Nancy; Nguyen, Long V.; Inui, Ken; Yang, Genyan; Creanga, Adrian; Wang, Li; Mai, Duong T.; Thor, Sharmi; Stevens, James; To, Thanh L.; Wentworth, David E.; Nguyen, Tung; Pham, Dong V.; Bryant, Juliet E.

    2016-01-01

    ABSTRACT Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs. IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and

  8. Cytogeography of the Humifusa clade of Opuntia s.s. Mill. 1754 (Cactaceae, Opuntioideae, Opuntieae): correlations with pleistocene refugia and morphological traits in a polyploid complex

    PubMed Central

    Majure, Lucas C.; Judd, Walter S.; Soltis, Pamela S.; Soltis, Douglas E.

    2012-01-01

    Abstract Ploidy has been well studied and used extensively in the genus Opuntia to determine species boundaries, detect evidence of hybridization, and infer evolutionary patterns. We carried out chromosome counts for all members of the Humifusa clade to ascertain whether geographic patterns are associated with differences in ploidy. We then related chromosomal data to observed morphological variability, polyploid formation, and consequently the evolutionary history of the clade. We counted chromosomes of 277 individuals from throughout the ranges of taxa included within the Humifusa clade, with emphasis placed on the widely distributed species, Opuntia humifusa (Raf.) Raf., 1820 s.l. and Opuntia macrorhiza Engelm., 1850 s.l. We also compiled previous counts made for species in the clade along with our new counts to plot geographic distributions of the polyploid and diploid taxa. A phylogeny using nuclear ribosomal ITS sequence data was reconstructed to determine whether ploidal variation is consistent with cladogenesis. We discovered that diploids of the Humifusa clade are restricted to the southeastern United States (U.S.), eastern Texas, and southeastern New Mexico. Polyploid members of the clade, however, are much more widely distributed, occurring as far north as the upper midwestern U.S. (e.g., Michigan, Minnesota, Wisconsin). Morphological differentiation, although sometimes cryptic, is commonly observed among diploid and polyploid cytotypes, and such morphological distinctions may be useful in diagnosing possible cryptic species. Certain polyploid populations of Opuntia humifusa s.l. and Opuntia macrorhiza s.l., however, exhibit introgressive morphological characters, complicating species delineations. Phylogenetically, the Humifusa clade forms two subclades that are distributed, respectively, in the southeastern U.S. (including all southeastern U.S. diploids, polyploid Opuntia abjecta Small, 1923, and polyploid Opuntia pusilla (Haw.) Haw., 1812) and the

  9. Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

    PubMed

    Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

    2009-05-01

    Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional

  10. Spatial Variation in Development of Epibenthic Assemblages in a Coastal Lagoon

    NASA Astrophysics Data System (ADS)

    Benedetti-Cecchi, L.; Rindi, F.; Bertocci, I.; Bulleri, F.; Cinelli, F.

    2001-05-01

    Spatial and temporal patterns in colonization of epibenthic assemblages were measured in a coastal lagoon on the west coast of Italy using recruitment panels. It was proposed that if the ecological processes influencing development of assemblages were homogeneous within the lagoon, then there should be no differences in mean cover of colonists nor in spatial patterns of variance in abundance in different areas of the lagoon. In contrast, heterogeneity in ecological processes affecting development would be revealed by spatial variability in colonization. To test these hypotheses, two sticks each with five replicate panels were placed 3-5 m apart in each of two sites 30-100 m apart in each of three locations 500-100 m apart; the experiment was repeated three times between April and December 1999, using new sites at each location each time. The results revealed considerable spatial variation in the structure of developing assemblages across locations. There were significant Location or Time×Location effects in the mean abundance of common taxa, such as Enteromorpha intestinalis , Ulva rigida, Cladophora spp., bryozoans and serpulids. Patterns in spatial variation differed among locations for these organisms. Collectively, the results supported a model of spatial heterogeneity in intensity of processes influencing patterns of recruitment and development of epibenthic assemblages in the Lagoon of Orbetello. The implications of these results for management of environmental problems in complex, variable habitats such as coastal lagoons, are discussed.

  11. Island characteristics within wetlands influence waterbird nest success and abundance

    USGS Publications Warehouse

    Hartman, Christopher; Ackerman, Joshua T.; Herzog, Mark

    2016-01-01

    Coastal waterbird populations are threatened by habitat loss and degradation from urban and agricultural development and forecasted sea level rise associated with climate change. Remaining wetlands often must be managed to ensure that waterbird habitat needs, and other ecosystem functions, are met. For many waterbirds, the availability of island nesting habitat is important for conserving breeding populations. We used linear mixed models to investigate the influence of pond and island landscape characteristics on nest abundance and nest success of American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanus), and Forster's terns (Sterna forsteri) in San Francisco Bay, California, USA, based on a 9-year dataset that included >9,000 nests. Nest abundance and nest success were greatest within ponds and on individual islands located either <1 km or >4 km from San Francisco Bay. Further, nest abundance was greater within ponds with relatively few islands, and on linear-shaped, highly elongated islands compared to more rounded islands. Nest success was greater on islands located away from the nearest surrounding pond levee. Compared to more rounded islands, linear islands contained more near-water habitat preferred by many nesting waterbirds. Islands located away from pond levees may provide greater protection from terrestrial egg and chick predators. Our results indicate that creating and maintaining a few, relatively small, highly elongated and narrow islands away from mainland levees, in as many wetland ponds as possible would be effective at providing waterbirds with preferred nesting habitat.

  12. Characterization of cross-clade monoclonal antibodies against H5N1 highly pathogenic avian influenza virus and their application to the antigenic analysis of diverse H5 subtype viruses.

    PubMed

    Gronsang, Dulyatad; Bui, Anh N; Trinh, Dai Q; Bui, Vuong N; Nguyen, Khong V; Can, Minh X; Omatsu, Tsutomu; Mizutani, Tetsuya; Nagai, Makoto; Katayama, Yukie; Thampaisarn, Rapeewan; Ogawa, Haruko; Imai, Kunitoshi

    2017-08-01

    H5N1 highly pathogenic avian influenza viruses (HPAIVs) are a threat to both animal and public health and require specific and rapid detection for prompt disease control. We produced three neutralizing anti-hemagglutinin (HA) monoclonal antibodies (mAbs) using two clades (2.2 and 2.5) of the H5N1 HPAIV isolated in Japan. Blocking immunofluorescence tests showed that each mAb recognized different epitopes; 3B5.1 and 3B5.2 mAbs against the clade 2.5 virus showed cross-clade reactivity to all 26 strains from clades 1, 2.2, 2.3.2.1, 2.3.2.1a, b, c and 2.3.4, suggesting that the epitope(s) recognized are conserved. Conversely, the 1G5 mAb against the clade 2.2 virus showed reactivity to only clades 1, 2.3.4 and 2.5 strains. An analysis of escape mutants, and some clades of the H5N1 viruses recognized by 3B5.1 and 3B5.2 mAbs, suggested that the mAbs bind to an epitope, including amino acid residues at position 162 in the HA1 protein (R162 and K162). Unexpectedly, however, when five Eurasian-origin H5 low-pathogenic AIV (LPAIV) strains with R162 were examined (EA-nonGsGD clade) as well as two American-origin strains (Am-nonGsGD clade), the mAb recognized only EA-nonGsGD clade strains. The R162 and K162 residues in the HA1 protein were highly conserved among 36 of the 43 H5N1 clades reported, including clades 2.3.2.1a and 2.3.2.1c that are currently circulating in Asia, Africa and Europe. The amino acid residues (158-PTIKRSYNNTNQE-170) in the HA1 protein are probably an epitope responsible for the cross-clade reactivity of the mAbs, considering the epitopes reported elsewhere. The 3B5.1 and 3B5.2 mAbs may be useful for the specific detection of H5N1 HPAIVs circulating in the field.

  13. A multiplex PCR method discriminating between the TYLCV and TYLCV-Mld clades of tomato yellow leaf curl virus.

    PubMed

    Lefeuvre, P; Hoareau, M; Delatte, H; Reynaud, B; Lett, J-M

    2007-09-01

    Tomato yellow leaf curl virus (TYLCV) is one of the causal agents of tomato yellow leaf curl disease (TYLCD) and can cause up to 100% yield losses in tomato fields. As TYLCV continues to spread, many isolates have been described in different parts of the world. Recently two closely related but distinct TYLCV clades, called TYLCV and TYLCV-Mld, have been identified. Isolates from those two clades differ mainly in the nucleotide sequences of their replication associated protein genes but do not display significantly different symptomatology. In order to improve monitoring of the rapidly expanding worldwide TYLCD epidemic, a multiplex polymerase chain reaction assay (mPCR) was developed. A set of three primers were designed to detect and characterize the TYLCV and TYLCV-Mld clade isolates. The specificity and sensitivity of the mPCR were validated on TYLCV infected tomato plants and Bemisia tabaci whiteflies. Being cheap, fast and highly sensitive this new diagnostic tool should greatly simplify efforts to trace the global spread of TYLCV.

  14. Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo).

    PubMed

    Cicero, C; Johnson, N K

    1998-10-01

    We constructed a molecular phylogeny for a clade of eye-ringed vireos (Vireo flavifrons and the V. solitarius complex) to examine existing hypotheses of speciation and ecological diversification. Complete sequences of the mtDNA cytochrome b gene were obtained from 47 individuals of this group plus four vireonid outgroups. Mean levels of sequence divergence in the clade varied from 0.29% to 5.7%. Differences were greatest between V. flavifrons and four taxa of 'V. solitarius'. The latter separated into three taxonomic, geographical and ecological groups: V. plumbeus plumbeus, V. cassinii cassinii, and V. solitarius solitarius plus V. solitarius alticola. These differed by an average of 2.6-3.2%. Populations within each group revealed low levels of sequence variation (x = 0.20%) and little geographical structuring. The mtDNA data generally corroborate results from allozymes. V. plumbeus shows a loss of yellow-green carotenoid pigmentation from the ancestral condition. The occupancy of relatively dry habitats by this species and V. cassinii represents a derived ecological shift from more-humid environments occupied by other species of vireonids. Ecological divergence in this clade occurred in allopatry and is associated with generic-level stability in morphometrics and foraging styles. Migratory behaviour and seasonal habitat shifts apparently evolved multiple times in vireos breeding in temperate environments. Present geographical and ecological distributions, and low levels of intrataxon genetic divergence, are hypothesized to be the result of postglacial regionalization of climate-plant associations and rapid northward expansion of breeding ranges.

  15. Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems.

    PubMed

    Wang, Jian-Hua; Lu, Jian; Zhang, Yu-Xuan; Wu, Jun; Luo, Yongming; Liu, Hao

    2018-04-01

    The overuse of antibiotics has posed a propagation of antibiotic resistance genes (ARGs) in aquaculture systems. This study firstly explored the ARGs profiles of the typical mariculture farms including conventional and recirculating systems using metagenomics approach. Fifty ARGs subtypes belonging to 21 ARGs types were identified, showing the wide-spectrum profiles of ARGs in the coastal industrial mariculture systems. ARGs with multiple antibiotics resistance have emerged in the mariculure systems. The co-occurrence pattern between ARGs and microbial taxa showed that Proteobacteria and Bacteroidetes were potential dominant hosts of ARGs in the industrial mariculture systems. Typical nitrifying bacteria such as Nitrospinae in mariculture systems also carried with some resistance genes. Relative abundance of ARGs in fish ponds and wastewater treatment units was relatively high. The investigation showed that industrial mariculture systems were important ARGs reservoirs in coastal area, indicating the critical role of recirculating systems in the terms of ARGs pollution control. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Highly pathogenic avian influenza H5N1 Clade 2.3.2.1c virus in migratory birds, 2014-2015.

    PubMed

    Bi, Yuhai; Chen, Jianjun; Zhang, Zhenjie; Li, Mingxin; Cai, Tianlong; Sharshov, Kirill; Susloparov, Ivan; Shestopalov, Alexander; Wong, Gary; He, Yubang; Xing, Zhi; Sun, Jianqing; Liu, Di; Liu, Yingxia; Liu, Lei; Liu, Wenjun; Lei, Fumin; Shi, Weifeng; Gao, George F

    2016-08-01

    A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015. Based on the genetic and phylogenetic analyses, the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA, a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin. The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain (A/Alberta/01/2014). Further analysis showed that similar viruses have been circulating in wild birds in China, Russia, Dubai (Western Asia), Bulgaria and Romania (Europe), as well as domestic poultry in some regions of Africa. The affected areas include the Central Asian, East Asian-Australasian, West Asian-East African, and Black Sea/Mediterranean flyways. These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds, thus posing a serious threat to wild birds and potentially humans.

  17. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

    PubMed Central

    Smith, Maria W.; Zeigler Allen, Lisa; Allen, Andrew E.; Herfort, Lydie; Simon, Holly M.

    2013-01-01

    The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1–0.8, 0.8–3, and 3–200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2–10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin

  18. Coastal Warning Display Program

    Science.gov Websites

    ! Boating Safety Beach Hazards Rip Currents Hypothermia Hurricanes Thunderstorms Lightning Coastal Flooding Tsunamis 406 EPIRB's National Weather Service Marine Forecasts COASTAL WARNING DISPLAY PROGRAM Marine COASTAL WARNING DISPLAY PROGRAM As of February 15, 1989, the National Weather Service retired its Coastal

  19. Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

    PubMed Central

    2012-01-01

    Background The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. Results The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma). Conclusions The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants. PMID:22316163

  20. Lake Superior Coastal Wetland Fish Assemblages and ...

    EPA Pesticide Factsheets

    The role of the coastal margin and the watershed context in defining the ecology of even very large lakes is increasingly being recognized and examined. Coastal wetlands are both important contributors to the biodiversity and productivity of large lakes and important mediators of the lake-basin connection. We explored wetland-watershed connections and their relationship to wetland function and condition using data collected from 37 Lake Superior wetlands spanning a substantial geographic and geomorphic gradient. While none of these wetlands are particularly disturbed, there were nevertheless clear relationships between watershed landuse and wetland habitat and biota, and these varied consistently across wetland type categories that reflected the strength of connection to the watershed. For example, water clarity and vegetation structure complexity declined with decreasing percent natural land cover, and these effects were strongest in riverine wetlands (having generally large watersheds and tributary-dominated hydrology) and weakest in lagoon wetlands (having generally small watersheds and lake-dominate hydrology). Fish abundance and species richness both increased with decreasing percent natural land cover while species diversity decreased, and again the effect was strongest in riverine wetlands. Lagoonal wetlands, which lack any substantial tributary, consistently harbored the fewest species of fish and a composition different from the more watershed-lin

  1. A NATIONAL COASTAL ASSESSMENT OF COASTAL SEDIMENT CONDITION

    EPA Science Inventory

    One element of the Environmental Monitoring and Assessment Program's National Coastal Assessment is to estimate the current status, extent, changes and trends in the condition of the Nation's coastal sediments on a national basis. Based on NCA monitoring activities from 1999-2001...

  2. Detection and Genomic Characterization of Motility in Lactobacillus curvatus: Confirmation of Motility in a Species outside the Lactobacillus salivarius Clade

    PubMed Central

    Cousin, Fabien J.; Lynch, Shónagh M.; Harris, Hugh M. B.; McCann, Angela; Lynch, Denise B.; Neville, B. Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito

    2014-01-01

    Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC 0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15°C and 37°C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus in the L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli. PMID:25501479

  3. Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.

    PubMed

    Cousin, Fabien J; Lynch, Shónagh M; Harris, Hugh M B; McCann, Angela; Lynch, Denise B; Neville, B Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito; O'Toole, Paul W

    2015-02-01

    Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

  4. Abundance and distribution of immature mosquitoes in urban rivers proximate to their larval habitats.

    PubMed

    Ma, Minghai; Huang, Minsheng; Leng, Peien

    2016-11-01

    Whether ecological restoration of polluted urban rivers would provide suitable breeding habitats for some mosquitoes was not clear yet. It was therefore important to determine how altered river conditions influence mosquito ecology. Monthly data on water quality and larval density were obtained to determine the effects of river systems on the distribution and abundance of immature mosquitoes in two coastal cities in Eastern China. In total, 5 species within two genera of mosquitoes were collected and identified in habitat with vegetation from three positive rivers. Culex pipiens pallens was the most abundant and widely distributed species. A new species (Culex fuscanus) was reported in certain districts. Physico-chemical parameters of river water were important, but not the only, set of influences on immature mosquito breeding. Aquatic vegetation could increase the likelihood of mosquito breeding while artificial aeration might prevent the approach of mosquitoes. Slow-moving water might be a new potential marginal habitat type for some Culex and Aedes albopictus. Variation of river system with ecological restoration might influence the abundance and distribution of immature mosquitoes. Copyright © 2016. Published by Elsevier B.V.

  5. Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics.

    PubMed

    Slater, Graham J; Goldbogen, Jeremy A; Pyenson, Nicholas D

    2017-05-31

    Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. © 2017 The Author(s).

  6. Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

    PubMed Central

    Goldbogen, Jeremy A.

    2017-01-01

    Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. PMID:28539520

  7. The Analysis of Phytoplankton Abundance Using Weibull Distribution (A Case Study in the Coastal Area of East Yapen in the Regency of Yapen Islands, Papua)

    ERIC Educational Resources Information Center

    Indrayani, Ervina; Dimara, Lisiard; Paiki, Kalvin; Reba, Felix

    2018-01-01

    The coastal waters of East Yapen is one of the spawning sites and areas of care for marine biota in Papua. Because of its very open location, it is widely used by human activities such as fishing, residential, industrial and cruise lines. This indirectly affects the balance of coastal waters condition of East Yapen that impact on the existence of…

  8. Challenges for accurate and prompt molecular diagnosis of clades of highly pathogenic avian influenza H5N1 viruses emerging in Vietnam.

    PubMed

    Slomka, Marek J; To, Thanh L; Tong, Hien H; Coward, Vivien J; Hanna, Amanda; Shell, Wendy; Pavlidis, Theo; Densham, Anstice L E; Kargiolakis, Georgios; Arnold, Mark E; Banks, Jill; Brown, Ian H

    2012-01-01

    Forty-six chickens and 48 ducks were sampled from four Vietnamese poultry premises in 2009 infected with H5N1 highly pathogenic avian influenza (HPAI) clade 2.3.2 and 2.3.4 viruses, which also differed by cleavage site (CS) sequences in their haemagglutinin (HA) genes. All clinical specimens (n=282), namely tracheal and cloacal swabs plus feathers, were tested by five Eurasian reverse-transcriptase AI RealTime polymerase chain reaction (RRT-PCR) methods. Bayesian modelling showed similar high sensitivity for the validated H5 HA2 RRT-PCR and a new modified M-gene RRT-PCR that utilizes lyophilized reagents. Both were more sensitive than the validated "wet" M-gene RRT-PCR. Another RRT-PCR, which targeted the H5-gene CS region, was effective for clade 2.3.4 detection, but severely compromised for clade 2.3.2 viruses. Reduced sensitivity of the H5 CS and "wet" M-gene RRT-PCRs correlated with mismatches between the target and the primer and/or probe sequences. However, the H5 HA2 RRT-PCR sensitively detected both clade 2.3.2 and 2.3.4 viruses, and agreed with N1 RRT-PCR results. Feather testing from diseased chicken and duck flocks by AI RRT-PCRs resulted in the most sensitive identification of H5N1 HPAI-infected birds. Evolution of new H5N1 HPAI clades remains a concern for currently affected Asian countries, but also for more distant regions where it is important to be prepared for new incursions of H5N1 HPAI viruses. Genetic evidence for adamantane resistance and sensitivity was also observed in isolates from both clades.

  9. Glucosylation and other biotransformations of T-2 toxin by yeasts of the Trichomonascus clade

    USDA-ARS?s Scientific Manuscript database

    Twenty-five yeasts assigned to the Trichomonascus clade (Saccharomycotina, Ascomycota), including three Trichomonascus species and 22 anamorphic species presently classified in Blastobotrys, were tested for their ability to convert T-2 toxin, a Fusarium trichothecene mycotoxin, to less toxic product...

  10. Developing Clade-Specific Microsatellite Markers: A Case Study in the Filamentous Fungal Genus Aspergillus

    USDA-ARS?s Scientific Manuscript database

    Microsatellite markers are highly variable and very commonly used in population genetics studies. However, microsatellite loci are typically poorly conserved and cannot be used in distant related species. Thus, development of clade-specific microsatellite markers would increase efficiency and allow ...

  11. Dark production of carbon monoxide (CO) from dissolved organic matter in the St. Lawrence estuarine system: Implication for the global coastal and blue water CO budgets

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Xie, Huixiang; Fichot, CéDric G.; Chen, Guohua

    2008-12-01

    We investigated the thermal (dark) production of carbon monoxide (CO) from dissolved organic matter (DOM) in the water column of the St. Lawrence estuarine system in spring 2007. The production rate, Qco, decreased seaward horizontally and downward vertically. Qco exhibited a positive, linear correlation with the abundance of chromophoric dissolved organic matter (CDOM). Terrestrial DOM was more efficient at producing CO than marine DOM. The temperature dependence of Qco can be characterized by the Arrhenius equation with the activation energies of freshwater samples being higher than those of salty samples. Qco remained relatively constant between pH 4-6, increased slowly between pH 6-8 and then rapidly with further rising pH. Ionic strength and iron chemistry had little influence on Qco. An empirical equation, describing Qco as a function of CDOM abundance, temperature, pH, and salinity, was established to evaluate CO dark production in the global coastal waters (depth < 200 m). The total coastal CO dark production from DOM was estimated to be from 0.46 to 1.50 Tg CO-C a-1 (Tg carbon from CO a-1). We speculated the global oceanic (coastal plus open ocean) CO dark production to be in the range from 4.87 to 15.8 Tg CO-C a-1 by extrapolating the coastal water-based results to blue waters (depth > 200 m). Both the coastal and global dark source strengths are significant compared to the corresponding photochemical CO source strengths (coastal: ˜2.9 Tg CO-C a-1; global: ˜50 Tg CO-C a-1). Steady state deepwater CO concentrations inferred from Qco and microbial CO uptake rates are <0.1 nmol L-1.

  12. Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing

    PubMed Central

    del Campo, Javier; Mallo, Diego; Massana, Ramon; de Vargas, Colomban; Richards, Thomas A.; Ruiz-Trillo, Iñaki

    2015-01-01

    Summary The opisthokonts are one of the major super-groups of eukaryotes. It comprises two major clades: 1) the Metazoa and their unicellular relatives and 2) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here we begin to address this gap by analyzing high throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyze the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant role of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). Furthermore, we describe a new lineage of marine fonticulids (MAFO) that appears to be abundant in sediments. Therefore, our work points to a greater potential ecological role for unicellular opisthokonts than previously appreciated in marine environments, both in water column and sediments, and also provides evidence of novel opisthokont phylogenetic lineages. This study highlights the importance of high throughput sequencing approaches to unravel the diversity and distribution of both known and novel eukaryotic lineages. PMID:25556908

  13. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea.

    PubMed

    Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

    2007-05-01

    Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and

  14. Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea▿

    PubMed Central

    Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

    2007-01-01

    Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56% ± 8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94% ± 2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and

  15. Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015.

    PubMed

    Nguyen, Diep T; Jang, Yunho; Nguyen, Tho D; Jones, Joyce; Shepard, Samuel S; Yang, Hua; Gerloff, Nancy; Fabrizio, Thomas; Nguyen, Long V; Inui, Ken; Yang, Genyan; Creanga, Adrian; Wang, Li; Mai, Duong T; Thor, Sharmi; Stevens, James; To, Thanh L; Wentworth, David E; Nguyen, Tung; Pham, Dong V; Bryant, Juliet E; Davis, C Todd

    2017-03-01

    Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs. IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and sporadic human

  16. Spatio-temporal distribution patterns of the epibenthic community in the coastal waters of Suriname

    NASA Astrophysics Data System (ADS)

    Willems, Tomas; De Backer, Annelies; Wan Tong You, Kenneth; Vincx, Magda; Hostens, Kris

    2015-10-01

    This study aimed to characterize the spatio-temporal patterns of the epibenthic community in the coastal waters of Suriname. Data were collected on a (bi)monthly basis in 2012-2013 at 15 locations in the shallow (<40 m) coastal area, revealing three spatially distinct species assemblages, related to clear gradients in some environmental parameters. A species-poor coastal assemblage was discerned within the muddy, turbid-water zone (6-20 m depth), dominated by Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Penaeoidea). Near the 30 m isobath, sediments were much coarser (median grain size on average 345±103 μm vs. 128±53 μm in the coastal assemblage) and water transparency was much higher (on average 7.6±3.5 m vs. 2.4±2.1 m in the coastal assemblage). In this zone, a diverse offshore assemblage was found, characterized by brittle stars (mainly Ophioderma brevispina and Ophiolepis elegans) and a variety of crabs, sea stars and hermit crabs. In between both zones, a transition assemblage was noted, with epibenthic species typically found in either the coastal or offshore assemblages, but mainly characterized by the absence of X. kroyeri. Although the epibenthic community was primarily structured in an on-offshore gradient related to depth, sediment grain size and sediment total organic carbon content, a longitudinal (west-east) gradient was apparent as well. The zones in the eastern part of the Suriname coastal shelf seemed to be more widely stretched along the on-offshore gradient. Although clear seasonal differences were noted in the environmental characteristics (e.g. dry vs. rainy season), this was not reflected in the epibenthic community structure. X. kroyeri reached very high densities (up to 1383 ind 1000 m-²) in the shallow coastal waters of Suriname. As X. kroyeri is increasingly exploited throughout its range, the current study provides the ecological context for its presence and abundance, which is crucial for an ecosystem approach and the

  17. Coastal mapping handbook

    USGS Publications Warehouse

    ,; ,; Ellis, Melvin Y.

    1978-01-01

    Passage of the Coastal Zone Management Act of 1972 focused attention on the Nation's coastal land and water areas. As plans for more effective management of the coastal zone evolved, it soon became apparent that improved maps and charts of these areas were needed. This handbook was prepared with the requirements of the entire coastal community in mind, giving greatest attention to the needs of coastal zone managers and planners at the State and local levels. Its principal objective is to provide general information and guidance; it is neither a textbook nor a technical manual, but rather a primer on coastal mapping. This handbook should help planners and managers of coastal programs to determine their mapping requirements, select the best maps and charts for their particular needs, and to deal effectively with personnel who gather data and prepare maps. The sections on "Sources of Assistance and Advice" and "Product and Data Sources" should be especially useful to all involved in mapping the coastal zone. Brief summaries of the mapping efforts of several State coastal zone management programs are included. "Future outlook" discusses anticipated progress and changes in mapping procedures and techniques. Illustrations are inserted, where appropriate, to illustrate the products and equipment discussed. Because of printing restrictions, the colors in map illustrations may vary from those in the original publication. The appendixes include substantial material which also should be of interest. In addition a glossary and an index are included to provide easy and quick access to the terms and concepts used in the text. For those interested in more technical detail than is provided in this handbook, the "Selected references" will be useful. Also, the publications of the professional societies listed in appendix 4 will provide technical information in detail.

  18. Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico

    PubMed Central

    Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto

    2015-01-01

    Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. PMID:26159533

  19. Facilitation influences patterns of perennial species abundance and richness in a subtropical dune system

    PubMed Central

    Dalotto, Cecilia E S; Sühs, Rafael B; Dechoum, Michele S; Pugnaire, Francisco I; Peroni, Nivaldo; Castellani, Tânia T

    2018-01-01

    Abstract Positive interactions in plant communities are under-reported in subtropical systems most likely because they are not identified as stressful environments. However, environmental factors or disturbance can limit plant growth in any system and lead to stressful conditions. For instance, salinity and low nutrient and water availability generate a gradient of stressful conditions in coastal systems depending on distance to shore. In a tropical coastal system in SE Brazil, we aimed to assess whether Guapira opposita, a shrub common in restinga environments, acted as nurse involved in ecological succession and which factors influenced its facilitation process. We sampled perennial species above 10 cm in height under the canopy of 35 G. opposita individuals and in neighbouring open areas. Shrub height, canopy area and distance to freshwater bodies were measured in the field, and distance to the ocean was obtained from aerial images. In addition, we measured the distance to the closest forest patch as a potential source of seeds. Plant abundance and species richness were higher under the canopy of G. opposita than in open areas. Facilitation by G. opposita was mainly determined by shrub height, which had a positive relationship with woody and bromeliads abundance and species richness while there was no relationship with the other factors. Overall, our data evidence that tropical environments may be highly stressful for plants and that nurse species play a key role in the regeneration of restinga environments, where their presence is critical to maintain ecosystem diversity and function. PMID:29644027

  20. Origin and Diversification of Major Clades in Parmelioid Lichens (Parmeliaceae, Ascomycota) during the Paleogene Inferred by Bayesian Analysis

    PubMed Central

    Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K.; Lumbsch, H. Thorsten; Crespo, Ana

    2011-01-01

    There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our

  1. Advertisement call of Scinax camposseabrai (Bokermann, 1968) (Anura: Hylidae), with comments on the call of three species of the Scinax ruber clade.

    PubMed

    Novaes, Gabriel; Zina, Juliana

    2016-02-25

    Scinax camposseabrai was allocated into the Scinax ruber clade by Caramaschi & Cardoso (2006) by overall similarities as snout not pointed, breeding in open areas, and an advertisement calls with multipulsed notes. This assumption about the call was based solely on an onomatopoeia provided by Bokermann (1968). Herein we provide a formal description of the advertisement call of S. camposseabrai and compare it with described calls of other S. ruber clade species. Additionally, we provide descriptions of the advertisement calls of three sympatric species of the S. ruber clade: S. eurydice (Bokermann), S. pachycrus (Miranda-Ribeiro) and S. cf. x-signatus.

  2. Gaining the necessary geologic, hydrologic, and geochemical understanding for additional brackish groundwater development, coastal San Diego, California, USA

    USGS Publications Warehouse

    Danskin, Wesley R.

    2012-01-01

    Local water agencies and the United States Geological Survey are using a combination of techniques to better understand the scant freshwater resources and the much more abundant brackish resources in coastal San Diego, California, USA. Techniques include installation of multiple-depth monitoring well sites; geologic and paleontological analysis of drill cuttings; geophysical logging to identify formations and possible seawater intrusion; sampling of pore-water obtained from cores; analysis of chemical constituents including trace elements and isotopes; and use of scoping models including a three-dimensional geologic framework model, rainfall-runoff model, regional groundwater flow model, and coastal density-dependent groundwater flow model. Results show that most fresh groundwater was recharged during the last glacial period and that the coastal aquifer has had recurring intrusions of fresh and saline water. These intrusions disguise the source, flowpaths, and history of ground water near the coast. The flow system includes a freshwater lens resting on brackish water; a 100-meter-thick flowtube of freshwater discharging under brackish estuarine water and above highly saline water; and broad areas of fine-grained coastal sediment filled with fairly uniform brackish water. Stable isotopes of hydrogen and oxygen indicate the recharged water flows through many kilometers of fractured crystalline rock before entering the narrow coastal aquifer.

  3. Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests.

    PubMed

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not.

  4. Seabird Nutrient Subsidies Benefit Non-Nitrogen Fixing Trees and Alter Species Composition in South American Coastal Dry Forests

    PubMed Central

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not. PMID:24466065

  5. Abundance and tidal behaviour of pelagic fish in the gateway to the Wadden Sea

    NASA Astrophysics Data System (ADS)

    Couperus, Bram; Gastauer, Sven; Fässler, Sascha M. M.; Tulp, Ingrid; van der Veer, Henk W.; Poos, Jan Jaap

    2016-03-01

    The shallow coast of The Netherlands is an important habitat for small pelagic fish. They form one of the major links between plankton and the higher trophic levels. Predatory fish, sea mammals and birds rely on small pelagic fish as a major food source. Currently, monitoring of fish in the Dutch coastal zone mainly focuses on demersal species, using bottom trawls and fykes. Four hydro-acoustic surveys were carried out in May and October 2010/2011 in the Marsdiep area, a relatively deep tidal inlet in the western Wadden Sea, to quantify abundances of pelagic fish. The aims of this study were to (1) describe temporal and vertical variations in fish distribution and school dimensions in relation to tide, and (2) estimate biomass of pelagic fish and their proportion to total fish biomass. The biomass of pelagic fish in the Marsdiep area ranged between 23 and 411 kg/ha. These were mainly sprat, but also young herring, anchovy and pilchard. The fish was scattered in small schools with volumes smaller than 5m3 and concentrated in the top 10 m below the surface. There was a clear effect of tidal cycle on school volume and fish abundance, with larger densities and larger schools at high tide compared to low tide. In May, sandeel contributed substantially to the pelagic assemblage, whereas in October sandeel was absent in the trawl catches, most likely because they stayed buried in the seabed from late summer to spring. The presence of pilchard and anchovy confirmed their re-establishment in the Southern North Sea and Wadden Sea. The abundance of pelagic fish exceeded the biomass of demersal fish in the western Wadden Sea by an order of magnitude. This finding is relevant for ecosystem studies. The fact that this study suggests that small pelagics outnumber demersal species to such a large extent calls for a rethinking of the allocation of monitoring effort in the Dutch coastal zone.

  6. Estimating the abundance of the Southern Hudson Bay polar bear subpopulation with aerial surveys

    USGS Publications Warehouse

    Obbard, Martyn E.; Stapleton, Seth P.; Middel, Kevin R.; Thibault, Isabelle; Brodeur, Vincent; Jutras, Charles

    2015-01-01

    The Southern Hudson Bay (SH) polar bear subpopulation occurs at the southern extent of the species’ range. Although capture–recapture studies indicate abundance was likely unchanged between 1986 and 2005, declines in body condition and survival occurred during the period, possibly foreshadowing a future decrease in abundance. To obtain a current estimate of abundance, we conducted a comprehensive line transect aerial survey of SH during 2011–2012. We stratified the study site by anticipated densities and flew coastal contour transects and systematically spaced inland transects in Ontario and on Akimiski Island and large offshore islands in 2011. Data were collected with double-observer and distance sampling protocols. We surveyed small islands in James Bay and eastern Hudson Bay and flew a comprehensive transect along the Québec coastline in 2012. We observed 667 bears in Ontario and on Akimiski Island and nearby islands in 2011, and we sighted 80 bears on offshore islands during 2012. Mark–recapture distance sampling and sight–resight models yielded an estimate of 860 (SE = 174) for the 2011 study area. Our estimate of abundance for the entire SH subpopulation (943; SE = 174) suggests that abundance is unlikely to have changed significantly since 1986. However, this result should be interpreted cautiously because of the methodological differences between historical studies (physical capture–recapture) and this survey. A conservative management approach is warranted given previous increases in duration of the ice-free season, which are predicted to continue in the future, and previously documented declines in body condition and vital rates.

  7. Projected Scenarios for Coastal First Nations' Fisheries Catch Potential under Climate Change: Management Challenges and Opportunities.

    PubMed

    Weatherdon, Lauren V; Ota, Yoshitaka; Jones, Miranda C; Close, David A; Cheung, William W L

    2016-01-01

    Studies have demonstrated ways in which climate-related shifts in the distributions and relative abundances of marine species are expected to alter the dynamics and catch potential of global fisheries. While these studies assess impacts on large-scale commercial fisheries, few efforts have been made to quantitatively project impacts on small-scale subsistence and commercial fisheries that are economically, socially and culturally important to many coastal communities. This study uses a dynamic bioclimate envelope model to project scenarios of climate-related changes in the relative abundance, distribution and richness of 98 exploited marine fishes and invertebrates of commercial and cultural importance to First Nations in coastal British Columbia, Canada. Declines in abundance are projected for most of the sampled species under both the lower (Representative Concentration Pathway [RCP] 2.6) and higher (RCP 8.5) emission scenarios (-15.0% to -20.8%, respectively), with poleward range shifts occurring at a median rate of 10.3 to 18.0 km decade(-1) by 2050 relative to 2000. While a cumulative decline in catch potential is projected coastwide (-4.5 to -10.7%), estimates suggest a strong positive correlation between the change in relative catch potential and latitude, with First Nations' territories along the northern and central coasts of British Columbia likely to experience less severe declines than those to the south. Furthermore, a strong negative correlation is projected between latitude and the number of species exhibiting declining abundance. These trends are shown to be robust to alternative species distribution models. This study concludes by discussing corresponding management challenges that are likely to be encountered under climate change, and by highlighting the value of joint-management frameworks and traditional fisheries management approaches that could aid in offsetting impacts and developing site-specific mitigation and adaptation strategies derived

  8. Projected Scenarios for Coastal First Nations’ Fisheries Catch Potential under Climate Change: Management Challenges and Opportunities

    PubMed Central

    Weatherdon, Lauren V.; Ota, Yoshitaka; Jones, Miranda C.; Close, David A.; Cheung, William W. L.

    2016-01-01

    Studies have demonstrated ways in which climate-related shifts in the distributions and relative abundances of marine species are expected to alter the dynamics and catch potential of global fisheries. While these studies assess impacts on large-scale commercial fisheries, few efforts have been made to quantitatively project impacts on small-scale subsistence and commercial fisheries that are economically, socially and culturally important to many coastal communities. This study uses a dynamic bioclimate envelope model to project scenarios of climate-related changes in the relative abundance, distribution and richness of 98 exploited marine fishes and invertebrates of commercial and cultural importance to First Nations in coastal British Columbia, Canada. Declines in abundance are projected for most of the sampled species under both the lower (Representative Concentration Pathway [RCP] 2.6) and higher (RCP 8.5) emission scenarios (-15.0% to -20.8%, respectively), with poleward range shifts occurring at a median rate of 10.3 to 18.0 km decade-1 by 2050 relative to 2000. While a cumulative decline in catch potential is projected coastwide (-4.5 to -10.7%), estimates suggest a strong positive correlation between the change in relative catch potential and latitude, with First Nations’ territories along the northern and central coasts of British Columbia likely to experience less severe declines than those to the south. Furthermore, a strong negative correlation is projected between latitude and the number of species exhibiting declining abundance. These trends are shown to be robust to alternative species distribution models. This study concludes by discussing corresponding management challenges that are likely to be encountered under climate change, and by highlighting the value of joint-management frameworks and traditional fisheries management approaches that could aid in offsetting impacts and developing site-specific mitigation and adaptation strategies derived

  9. Coastal Modeling System

    DTIC Science & Technology

    2015-11-04

    Coastal Inlets Research Program Coastal Modeling System The work unit develops the Coastal Modeling System ( CMS ) and conducts basic research to...further understanding of sediment transport under mixed oceanic and atmospheric forcing. The CMS is a suite of coupled two-dimensional numerical...models for simulations of waves, hydrodynamics, salinity and sediment transport, and morphology change. The CMS was identified by the USACE Hydraulics

  10. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type

    USGS Publications Warehouse

    Gregg, Jacob; Thompson, Rachel L.; Purcell, Maureen; Friedman, Carolyn S.; Hershberger, Paul

    2016-01-01

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1–5.8S–ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

  11. 75 FR 22103 - Atlantic Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark Fishery

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-27

    ... Coastal Fisheries Cooperative Management Act Provisions; Atlantic Coastal Shark Fishery AGENCY: National... Atlantic Coastal Fisheries Cooperative Management Act (Act), NMFS, upon a delegation of authority from the... Plan for Atlantic Coastal Sharks (Plan) and that the measures New Jersey has failed to implement and...

  12. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.

    ABSTRACT Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium , which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. Themore » response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. IMPORTANCE Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic

  13. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

    DOE PAGES

    Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.; ...

    2017-11-14

    ABSTRACT Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium , which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. Themore » response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. IMPORTANCE Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic

  14. High Local Diversity of Trypanosoma in a Common Bat Species, and Implications for the Biogeography and Taxonomy of the T. cruzi Clade

    PubMed Central

    Kalko, Elisabeth K. V.; Cottontail, Iain; Wellinghausen, Nele; Tschapka, Marco; Perkins, Susan L.

    2014-01-01

    The Trypanosoma cruzi clade is a group of parasites that comprises T. cruzi sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat Artibeus jamaicensis from the Panamá Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the T. cruzi clade. A small monophyletic group of three putative Trypanosoma species places at the base of the clade phylogeny, providing evidence for at least five independent colonization events of these parasites into the New World. Artibeus jamaicensis presents a high diversity of these blood parasites and is the vertebrate with the highest number of putative trypanosome species reported from a single locality. Our results emphasize the need for continued efforts to survey mammalian trypanosomes. PMID:25268381

  15. Phylogenetic Clades 6 and 8 of Enterohemorrhagic Escherichia coli O157:H7 With Particular stx Subtypes are More Frequently Found in Isolates From Hemolytic Uremic Syndrome Patients Than From Asymptomatic Carriers

    PubMed Central

    Iyoda, Sunao; Manning, Shannon D.; Seto, Kazuko; Kimata, Keiko; Isobe, Junko; Etoh, Yoshiki; Ichihara, Sachiko; Migita, Yuji; Ogata, Kikuyo; Honda, Mikiko; Kubota, Tsutomu; Kawano, Kimiko; Matsumoto, Kazutoshi; Kudaka, Jun; Asai, Norio; Yabata, Junko; Tominaga, Kiyoshi; Terajima, Jun; Morita-Ishihara, Tomoko; Izumiya, Hidemasa; Ogura, Yoshitoshi; Saitoh, Takehito; Iguchi, Atsushi; Kobayashi, Hideki; Hara-Kudo, Yukiko; Ohnishi, Makoto; Arai, Reiko; Kawase, Masao; Asano, Yukiko; Asoshima, Nanami; Chiba, Kazuki; Furukawa, Ichiro; Kuroki, Toshiro; Hamada, Madoka; Harada, Seiya; Hatakeyama, Takashi; Hirochi, Takashi; Sakamoto, Yumiko; Hiroi, Midori; Takashi, Kanda; Horikawa, Kazumi; Iwabuchi, Kaori; Kameyama, Mitsuhiro; Kasahara, Hitomi; Kawanishi, Shinya; Kikuchi, Koji; Ueno, Hiroyuki; Kitahashi, Tomoko; Kojima, Yuka; Konishi, Noriko; Obata, Hiromi; Kai, Akemi; Kono, Tomomi; Kurazono, Takayuki; Matsumoto, Masakado; Matsumoto, Yuko; Nagai, Yuhki; Naitoh, Hideki; Nakajima, Hiroshi; Nakamura, Hiromi; Nakane, Kunihiko; Nishi, Keiko; Saitoh, Etsuko; Satoh, Hiroaki; Takamura, Mitsuteru; Shiraki, Yutaka; Tanabe, Junichi; Tanaka, Keiko; Tokoi, Yuki; Yatsuyanagi, Jun

    2014-01-01

    Background  Enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection causes severe diseases such as bloody diarrhea and hemolytic uremic syndrome (HUS). Although EHEC O157:H7 strains have exhibited high genetic variability, their abilities to cause human diseases have not been fully examined. Methods  Clade typing and stx subtyping of EHEC O157:H7 strains, which were isolated in Japan during 1999–2011 from 269 HUS patients and 387 asymptomatic carriers (ACs) and showed distinct pulsed-field gel electrophoresis patterns, were performed to determine relationships between specific lineages and clinical presentation. Results  Clades 6 and 8 strains were more frequently found among the isolates from HUS cases than those from ACs (P = .00062 for clade 6, P < .0001 for clade 8). All clade 6 strains isolated from HUS patients harbored stx2a and/or stx2c, whereas all clade 8 strains harbored either stx2a or stx2a/stx2c. However, clade 7 strains were predominantly found among the AC isolates but less frequently found among the HUS isolates, suggesting a significant association between clade 7 and AC (P < .0001). Logistic regression analysis revealed that 0–9 year old age is a significant predictor of the association between clade 8 and HUS. We also found an intact norV gene, which encodes for a nitric oxide reductase that inhibits Shiga toxin activity under anaerobic condition, in all clades 1–3 isolates but not in clades 4–8 isolates. Conclusions  Early detection of EHEC O157:H7 strains that belonged to clades 6/8 and harbored specific stx subtypes may be important for defining the risk of disease progression in EHEC-infected 0- to 9-year-old children. PMID:25734131

  16. Restoring Coastal Plants to Improve Global Carbon Storage: Reaping What We Sow

    PubMed Central

    Irving, Andrew D.; Connell, Sean D.; Russell, Bayden D.

    2011-01-01

    Long-term carbon capture and storage (CCS) is currently considered a viable strategy for mitigating rising levels of atmospheric CO2 and associated impacts of global climate change. Until recently, the significant below-ground CCS capacity of coastal vegetation such as seagrasses, salt marshes, and mangroves has largely gone unrecognized in models of global carbon transfer. However, this reservoir of natural, free, and sustainable carbon storage potential is increasingly jeopardized by alarming trends in coastal habitat loss, totalling 30–50% of global abundance over the last century alone. Human intervention to restore lost habitats is a potentially powerful solution to improve natural rates of global CCS, but data suggest this approach is unlikely to substantially improve long-term CCS unless current restoration efforts are increased to an industrial scale. Failure to do so raises the question of whether resources currently used for expensive and time-consuming restoration projects would be more wisely invested in arresting further habitat loss and encouraging natural recovery. PMID:21479244

  17. Revegetation increase bird diversity in coastal area of Socorejo, Tuban, East Java - Indonesia

    NASA Astrophysics Data System (ADS)

    Lestari, Yeni Indah; Edi, Wasito; Alivvy, Alkautsar; Ibadah, Acib Setia; Sari, Fadina Yuliana; Nuraini, Finda; Yanuar, Ahmad; Satriyono, Agus; Riany, Citra Fitrie; Saptarini, Dian; Muzaki, Farid Kamal

    2017-06-01

    Study to address positive impact of revegetation program to increasing diversity of bird had been conducted in coastal area of Socorejo, Tuban - Indonesia. Field observation conducted during April 2011 (representing pre-revegetation period), April 2015 and May 2016 (representing post-revegetation period). A belt transect (500 meter long and 50 meter width) was used to survey the abundance and species composition of birds community. In general, we identified at least 51 bird species from three observation times. From 2011 to 2016, the numbers of the birds identified are 23, 37 and 37 species; while the Shannon-Wiener diversity indices (H') are 1.865, 2.071 and 2.957, respectively. In addition, there are 11 national or internationally protected species, 3 Indonesian endemic species and 12 migratory species occurred in the area. As a conclusion, the coastal revegetation program provides positive impact by generating habitat function for bird community.

  18. Can treefrog phylogeographical clades and species' phylogenetic topologies be recovered by bioacoustical analyses?

    PubMed

    Forti, Lucas Rodriguez; Lingnau, Rodrigo; Encarnação, Lais Carvalho; Bertoluci, Jaime; Toledo, Luís Felipe

    2017-01-01

    Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic

  19. Can treefrog phylogeographical clades and species’ phylogenetic topologies be recovered by bioacoustical analyses?

    PubMed Central

    Forti, Lucas Rodriguez; Lingnau, Rodrigo; Encarnação, Lais Carvalho; Bertoluci, Jaime; Toledo, Luís Felipe

    2017-01-01

    Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic

  20. The Coastal Ocean Prediction Systems program: Understanding and managing our coastal ocean

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Eden, H.F.; Mooers, C.N.K.

    1990-06-01

    The goal of COPS is to couple a program of regular observations to numerical models, through techniques of data assimilation, in order to provide a predictive capability for the US coastal ocean including the Great Lakes, estuaries, and the entire Exclusive Economic Zone (EEZ). The objectives of the program include: determining the predictability of the coastal ocean and the processes that govern the predictability; developing efficient prediction systems for the coastal ocean based on the assimilation of real-time observations into numerical models; and coupling the predictive systems for the physical behavior of the coastal ocean to predictive systems for biological,more » chemical, and geological processes to achieve an interdisciplinary capability. COPS will provide the basis for effective monitoring and prediction of coastal ocean conditions by optimizing the use of increased scientific understanding, improved observations, advanced computer models, and computer graphics to make the best possible estimates of sea level, currents, temperatures, salinities, and other properties of entire coastal regions.« less

  1. Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems.

    PubMed

    Lynn, Tin Mar; Ge, Tida; Yuan, Hongzhao; Wei, Xiaomeng; Wu, Xiaohong; Xiao, Keqing; Kumaresan, Deepak; Yu, San San; Wu, Jinshui; Whiteley, Andrew S

    2017-04-01

    CO 2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14 C ( 14 C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of 14 C-labeled soil organic carbon ( 14 C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14 C-SOC level, and 14 C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO 2 -fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

  2. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C

    PubMed Central

    Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

    2016-01-01

    Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies. PMID:27275832

  3. A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes).

    PubMed

    Bertram, Miranda R; Hamer, Sarah A; Hartup, Barry K; Snowden, Karen F; Medeiros, Matthew C; Outlaw, Diana C; Hamer, Gabriel L

    2017-04-01

    The unicellular blood parasites in the order Haemosporida are highly diverse, infect many vertebrates, are responsible for a large disease burden among humans and animals, and have reemerged as an important model system to understand the evolutionary and ecological dynamics of host-parasite interactions. The phylogenetics and systematics of Haemosporida are limited by poor sampling of different vertebrate host taxa. We surveyed the Haemosporida of wild whooping cranes (Grus americana) and sandhill cranes (Grus canadensis) (Aves: Gruiformes) using a combination of morphological and molecular approaches. We identified Haemoproteus antigonis in blood smears based on published morphological descriptions. Phylogenetic analysis based on partial cytochrome b (cytb) and cytochrome oxidase (coI) sequences placed H. antigonis parasites in a novel clade, distinct from all avian Haemosporida genera for which cytb and/or coI sequences are available. Molecular clock and divergence estimates suggest this crane clade may represent a new genus. This is the first molecular description of H. antigonis and the first report of H. antigonis in wild whooping cranes, an endangered bird in North America. Further sampling of Haemosporida, especially from hosts of the Gruiformes and other poorly sampled orders, will help to resolve the relationship of the H. antigonis clade to other avian Haemosporida genera. Our study highlights the potential of sampling neglected host species to discover novel lineages of diverse parasite groups. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

    USGS Publications Warehouse

    Holmes, Dawn E.; O'Neil, Regina A.; Vrionis, Helen A.; N'Guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll , Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

    2007-01-01

    There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

  5. Resilience from coastal protection.

    PubMed

    Ewing, Lesley C

    2015-10-28

    Coastal areas are important residential, commercial and industrial areas; but coastal hazards can pose significant threats to these areas. Shoreline/coastal protection elements, both built structures such as breakwaters, seawalls and revetments, as well as natural features such as beaches, reefs and wetlands, are regular features of a coastal community and are important for community safety and development. These protection structures provide a range of resilience to coastal communities. During and after disasters, they help to minimize damages and support recovery; during non-disaster times, the values from shoreline elements shift from the narrow focus on protection. Most coastal communities have limited land and resources and few can dedicate scarce resources solely for protection. Values from shore protection can and should expand to include environmental, economic and social/cultural values. This paper discusses the key aspects of shoreline protection that influence effective community resilience and protection from disasters. This paper also presents ways that the economic, environmental and social/cultural values of shore protection can be evaluated and quantified. It presents the Coastal Community Hazard Protection Resilience (CCHPR) Index for evaluating the resilience capacity to coastal communities from various protection schemes and demonstrates the use of this Index for an urban beach in San Francisco, CA, USA. © 2015 The Author(s).

  6. Predicting impact of SLR on coastal flooding in Banda Aceh coastal defences

    NASA Astrophysics Data System (ADS)

    Al'ala, Musa; Syamsidik, Kato, Shigeru

    2017-10-01

    Banda Aceh is a low-lying city located at the northern tip of Sumatra Island and situated at the conjuncture of Malacca Strait and the Andaman Sea. A Sea Level Rise (SLR) rate at 7 mm/year has been observed around this region. In the next 50 years, this city will face a serious challenge to encounter impacts of the sea level rise, such as frequent coastal floodings. This study is aimed at estimating impacts of the sea level rise induced coastal floodings on several types of coastal structures and city drainage system. Numerical simulations of Delft3D were applied to investigate the influence of the gradual sea level rise in 50 years. The hydrodynamic process of coastal flooding and sediment transport were simulated by Delft3D-Flow. Topography and bathymetry data were collected from GEBCO and updated with the available nautical chart (DISHIDROS, JICA, and field measurements). Hydrodynamic process gains the flow process revealing the level of the sea water intrusion also observed in the model. Main rivers (Krueng Aceh, Krueng Neng, and Alue Naga Flood Canal) and the drainage system were observed to see the tides effects on coastal structures and drainage system. The impact on coastal community focusing on affected area, shoreline retreat, the rate of sea intrusion was analyzed with spatial tools. New coastal line, coastal flooding vulnerable area, and the community susceptibility properties map influenced by 50 years sea level rise is produced. This research found that the city needs to address strategies to anticipate the exacerbating impacts of the sea level rise by managing its coastal spatial planning and modify its drainage system, especially at the drainage outlets.

  7. Ecologically Enhancing Coastal Infrastructure

    NASA Astrophysics Data System (ADS)

    Mac Arthur, Mairi; Naylor, Larissa; Hansom, Jim; Burrows, Mike; Boyd, Ian

    2017-04-01

    Hard engineering structures continue to proliferate in the coastal zone globally in response to increasing pressures associated with rising sea levels, coastal flooding and erosion. These structures are typically plain-cast by design and function as poor ecological surrogates for natural rocky shores which are highly topographically complex and host a range of available microhabitats for intertidal species. Ecological enhancement mitigates some of these negative impacts by integrating components of nature into the construction and design of these structures to improve their sustainability, resilience and multifunctionality. In the largest UK ecological enhancement trial to date, 184 tiles (15x15cm) of up to nine potential designs were deployed on vertical concrete coastal infrastructure in 2016 at three sites across the UK (Saltcoats, Blackness and Isle of Wight). The surface texture and complexity of the tiles were varied to test the effect of settlement surface texture at the mm-cm scale of enhancement on the success of colonisation and biodiversity in the mid-upper intertidal zone in order to answer the following experimental hypotheses: • Tiles with mm-scale geomorphic complexity will have greater barnacle abundances • Tiles with cm-scale geomorphic complexity will have greater species richness than mm-scale tiles. A range of methods were used in creating the tile designs including terrestrial laser scanning of creviced rock surfaces to mimic natural rocky shore complexity as well as artificially generated complexity using computer software. The designs replicated the topographic features of high ecological importance found on natural rocky shores and promoted species recruitment and community composition on artificial surfaces; thus enabling us to evaluate biological responses to geomorphic complexity in a controlled field trial. At two of the sites, the roughest tile designs (cm scale) did not have the highest levels of barnacle recruits which were

  8. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (North Atlantic)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Buckley, J.

    1989-08-01

    Species profiles are literature summaries of the taxonomy, life history, and environmental requirements of coastal fishes and aquatic invertebrates. They are designed to assist with environmental impact assessments. The rainbow smelt is an abundant forage fish for commercially and recreationally valuable fishes such as striped bass and bluefish on the East Coast and several species of salmon and trout in the Great Lakes. The rainbow smelt also supports an important sportfishery throughout most of its range. In 1976, the total smelt harvest in the coastal waters of New England was 105,000 lb. Coastal rainbow smelt are anadromous, spawning in freshwatermore » and maturing in saline water. Spawning peaks in spring. Salinities above 12 ppt were fatal to eggs. Reported fecundities are 7,000 to 44,000 eggs per female. Smelt are always found in shallow water (<6 m deep) and within 2 km of the shore. Larval and juvenile smelt along the coast feed on planktonic crustaceans. Larger juveniles and adults feed on euphausiids, amphipods, on planktonic crustaceans. Larger juveniles and adults feed on euphausiids, amphipods, polychaetes, and fish. Smelt move locally to search for optimum water temperatures. 46 refs., 2 figs., 1 tab.« less

  9. Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.

    PubMed

    Garcés-Ayala, Fabiola; Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto; Ramirez-González, José Ernesto

    2015-07-09

    Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. Copyright © 2015 Garcés-Ayala et al.

  10. Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages

    PubMed Central

    Su, Chunlei; Khan, Asis; Zhou, Peng; Majumdar, Debashree; Ajzenberg, Daniel; Dardé, Marie-Laure; Zhu, Xing-Quan; Ajioka, James W.; Rosenthal, Benjamin M.; Dubey, Jitender P.; Sibley, L. David

    2012-01-01

    Marked phenotypic variation characterizes isolates of Toxoplasma gondii, a ubiquitous zoonotic parasite that serves as an important experimental model for studying apicomplexan parasites. Progress in identifying the heritable basis for clinically and epidemiologically significant differences requires a robust system for describing and interpreting evolutionary subdivisions in this prevalent pathogen. To develop such a system, we have examined more than 950 isolates collected from around the world and genotyped them using three independent sets of polymorphic DNA markers, sampling 30 loci distributed across all nuclear chromosomes as well as the plastid genome. Our studies reveal a biphasic pattern consisting of regions in the Northern Hemisphere where a few, highly clonal and abundant lineages predominate; elsewhere, and especially in portions of South America are characterized by a diverse assemblage of less common genotypes that show greater evidence of recombination. Clustering methods were used to organize the marked genetic diversity of 138 unique genotypes into 15 haplogroups that collectively define six major clades. Analysis of gene flow indicates that a small number of ancestral lineages gave rise to the existing diversity through a process of limited admixture. Identification of reference strains for these major groups should facilitate future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission. PMID:22431627

  11. The Effect of Phylogeny, Environment and Morphology on Communities of a Lianescent Clade (Bignonieae-Bignoniaceae) in Neotropical Biomes

    PubMed Central

    Alcantara, Suzana; Ree, Richard H.; Martins, Fernando R.; Lohmann, Lúcia G.

    2014-01-01

    The influence of ecological traits to the distribution and abundance of species is a prevalent issue in biodiversity science. Most studies of plant community assembly have focused on traits related to abiotic aspects or direct interactions among plants, with less attention paid to ignore indirect interactions, as those mediated by pollinators. Here, we assessed the influence of phylogeny, habitat, and floral morphology on ecological community structure in a clade of Neotropical lianas (tribe Bignonieae, Bignoniaceae). Our investigation was guided by the long-standing hypothesis that habitat specialization has promoted speciation in Bignonieae, while competition for shared pollinators influences species co-occurrence within communities. We analyzed a geo-referenced database for 94 local communities occurring across the Neotropics. The effect of floral morphological traits and abiotic variables on species co-occurrence was investigated, taking into account phylogenetic relationships. Habitat filtering seems to be the main process driving community assembly in Bignonieae, with environmental conditions limiting species distributions. Differing specialization to abiotic conditions might have evolved recently, in contrast to the general pattern of phylogenetic clustering found in communities of other diverse regions. We find no evidence that competition for pollinators affects species co-occurrence; instead, pollinator occurrence seems to have acted as an “environmental filter” in some habitats. PMID:24594706

  12. Multilocus molecular phylogeny of the ornamental wood-eating catfishes (Siluriformes, Loricariidae, Panaqolus and Panaque) reveals undescribed diversity and parapatric clades.

    PubMed

    Lujan, Nathan K; Cramer, Christian A; Covain, Raphael; Fisch-Muller, Sonia; López-Fernández, Hernán

    2017-04-01

    Approximately two-dozen species in three genera of the Neotropical suckermouth armored catfish family Loricariidae are the only described fishes known to specialize on diets consisting largely of wood. We conducted a molecular phylogenetic analysis of 10 described species and 14 undescribed species or morphotypes assigned to the wood-eating catfish genus Panaqolus, and four described species and three undescribed species or morphotypes assigned to the distantly related wood-eating catfish genus Panaque. Our analyses included individuals and species from both genera that are broadly distributed throughout tropical South America east of the Andes Mountains and 13 additional genera hypothesized to have also descended from the most recent common ancestor of Panaqolus and Panaque. Bayesian and maximum likelihood analyses of two mitochondrial and three nuclear loci totaling 4293bp confirmed respective monophyly of Panaqolus, exclusive of the putative congener 'Panaqolus' koko, and Panaque. Members of Panaqolus sensu stricto were distributed across three strongly monophyletic clades: a clade of 10 generally darkly colored, lyretail species distributed across western headwaters of the Amazon Basin, a clade of three irregularly and narrowly banded species from the western Orinoco Basin, and a clade of 11 generally brown, broadly banded species that are widely distributed throughout the Amazon Basin. We erect new subgenera for each of these clades and a new genus for the morphologically, biogeographically and ecologically distinct species 'Panaqolus' koko. Our finding that perhaps half of the species-level diversity in the widespread genus Panaqolus remains undescribed illustrates the extent to which total taxonomic diversity of small and philopatric, yet apparently widely distributed, Amazonian fishes may remain underestimated. Ranges for two Panaqolus subgenera and the genus Panaque overlap with the wood-eating genus Cochliodon in central Andean tributaries of the upper

  13. Novel reassortant clade 2.3.4.4 avian influenza A (H5N8) virus in a grey heron in South Korea in 2017.

    PubMed

    Woo, Chanjin; Kwon, Jung-Hoon; Lee, Dong-Hun; Kim, Youngsik; Lee, Kwanghee; Jo, Seong-Deok; Son, Ki Dong; Oem, Jae-Ku; Wang, Seung-Jun; Kim, Yongkwan; Shin, Jeonghwa; Song, Chang-Seon; Jheong, Weonhwa; Jeong, Jipseol

    2017-12-01

    We report the identification of a novel reassortant clade 2.3.4.4 H5N8 virus from a dead grey heron in Korea in 2017. Outbreaks of clade 2.3.4.4 H5 HPAIVs have been reported worldwide, and they have evolved into multiple genotypes among wild birds. Phylogenetic analysis indicated that this virus likely originated from Qinghai Lake and Western Siberia and further evolved through reassortment with Eurasian LPAI during the 2016 fall migration of wild birds. Enhanced surveillance and comparative genetic analysis will help to monitor the further evolution and dissemination of clade 2.3.4.4 HPAIVs.

  14. New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria.

    PubMed

    Zhou, Zhichao; Chen, Jing; Meng, Han; Dvornyk, Volodymyr; Gu, Ji-Dong

    2017-02-01

    PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH 4 + and NH 4 + /Σ(NO 3 - + NO 2 - ) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox

  15. Formulating a coastal zone health metric for landuse impact management in urban coastal zones.

    PubMed

    Anilkumar, P P; Varghese, Koshy; Ganesh, L S

    2010-11-01

    The need for ICZM arises often due to inadequate or inappropriate landuse planning practices and policies, especially in urban coastal zones which are more complex due to the larger number of components, their critical dimensions, attributes and interactions. A survey of literature shows that there is no holistic metric for assessing the impacts of landuse planning on the health of a coastal zone. Thus there is a need to define such a metric. The proposed metric, CHI (Coastal zone Health Indicator), developed on the basis of coastal system sustainability, attempts to gauge the health status of any coastal zone. It is formulated and modeled through an expert survey and pertains to the characteristic components of coastal zones, their critical dimensions, and relevant attributes. The proposed metric is applied to two urban coastal zones and validated. It can be used for more coast friendly and sustainable landuse planning/masterplan preparation and thereby for the better management of landuse impacts on coastal zones. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. The evolutionary dynamics of highly pathogenic avian influenza H5N1 in south-central Vietnam reveals multiple clades evolving from Chinese and Cambodian viruses.

    PubMed

    Nguyen, Tinh Huu; Than, Van Thai; Thanh, Hien Dang; Nguyen, Van Quang; Nguyen, Kim Hue; Nguyen, Duc Tan; Park, Jong-Hwa; Chung, In Sik; Jeong, Dae Gwin; Chang, Kyu-Tae; Oh, Tae Kwang; Kim, Wonyong

    2015-10-01

    In Vietnam, highly pathogenic avian influenza (HPAI), such as that caused by H5N1 viruses, is the most highly contagious infectious disease that has been affecting domestic poultry in recent years. Vietnam might be an evolutionary hotspot and a potential source of globally pandemic strains. However, few studies have reported viruses circulating in the south-central region of Vietnam. In the present study, 47 H5N1-positive samples were collected from both vaccinated and unvaccinated poultry farms in the South Central Coast region of Vietnam during 2013-2014, and their genetic diversity was analyzed. A common sequence motif for HPAI virus was identified at HA-cleavage sites in all samples: either RERRRKR/G (clades 2.3.2.1c and 2.3.2.1a) or REGRRKKR/G (clade 1.1.2). Phylogenetic analysis of HA genes identified three clades of HPAI H5N1: 1.1.2 (n=1), 2.3.2.1a (n=1), and 2.3.2.1c (n=45). The phylogenetic analysis indicated that these Vietnamese clades may have evolved from Chinese and Cambodian virus clades isolated in 2012-2013 but are less closely related to the clades detected from the Tyva Republic, Bulgaria, Mongolia, Japan, and Korea in 2009-2011. Detection of the coexistence of virus clades 2.3.2.1 and the very virulent 1.1.2 in the south-central regions suggests their local importance and highlights concerns regarding their spread, both northwards and southwards, as well as the potential for reassortment. The obtained data highlight the importance of regular identification of viral evolution and the development and use of region-specific vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Predator decline leads to decreased stability in a coastal fish community.

    PubMed

    Britten, Gregory L; Dowd, Michael; Minto, Cóilín; Ferretti, Francesco; Boero, Ferdinando; Lotze, Heike K

    2014-12-01

    Fisheries exploitation has caused widespread declines in marine predators. Theory predicts that predator depletion will destabilise lower trophic levels, making natural communities more vulnerable to environmental perturbations. However, empirical evidence has been limited. Using a community matrix model, we empirically assessed trends in the stability of a multispecies coastal fish community over the course of predator depletion. Three indices of community stability (resistance, resilience and reactivity) revealed significantly decreasing stability concurrent with declining predator abundance. The trophically downgraded community exhibited weaker top-down control, leading to predator-release processes in lower trophic levels and increased susceptibility to perturbation. At the community level, our results suggest that high predator abundance acts as a stabilising force to the naturally stochastic and highly autocorrelated dynamics in low trophic species. These findings have important implications for the conservation and management of predators in marine ecosystems and provide empirical support for the theory of predatory control. © 2014 John Wiley & Sons Ltd/CNRS.

  18. Patterns of woody plant invasion in an Argentinean coastal grassland

    NASA Astrophysics Data System (ADS)

    Alberio, Constanza; Comparatore, Viviana

    2014-01-01

    Coastal dune grasslands are fragile ecosystems that have historically been subjected to various types of uses and human activities. In Buenos Aires Province (Argentina), these areas are frequently afforested for urban and touristic development. The introduction and subsequent spread of exotic tree species is one of the main threats to conservation of natural grasslands as invasive trees strongly transform their structure and composition. The aim of this study was to identify patterns of woody plant invasion comparing plant communities and environmental variables between invaded and non-invaded areas surrounding the coastal village of Mar Azul, Argentina. Coastal grasslands in this area are being invaded by Populus alba (white poplar) and Acacia longifolia (coast wattle). The height of the saplings and the richness of the accompanying vegetation were evaluated in relation to the distance from the edge of the mature tree patches. Also, the cover, richness and diversity of all species in the invaded and non-invaded areas were measured, as well as soil pH, temperature and particle size. Negative correlations were found between the height of the saplings and distance to mature tree patches in all areas. The richness of the accompanying vegetation was negatively and positively correlated with the distance from the poplar and acacia area, respectively. The most abundant native species was Cortaderia selloana. Less cover, richness and diversity of native plant species and greater soil particle size were found in invaded areas, where the proportion of bare soil was higher. Also, a higher proportion of leaf litter in the invaded areas was registered. The results emphasize the invasive capacity of P. alba and A. longifolia advancing on the native communities and reducing their richness. Knowledge of the impact of invasive woody plants in coastal grasslands is important to design active management strategies for conservation purposes.

  19. ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

    USGS Publications Warehouse

    Zargar, Kamrun; Conrad, Alison; Bernick, David L.; Lowe, Todd M.; Stolc, Viktor; Hoeft, Shelley; Oremland, Ronald S.; Stolz, John; Saltikov, Chad W.

    2012-01-01

    Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arxA was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arxA-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.

  20. Evidence of a Native Northwest Atlantic COI Haplotype Clade in the Cryptogenic Colonial Ascidian Botryllus schlosseri.

    PubMed

    Yund, Philip O; Collins, Catherine; Johnson, Sheri L

    2015-06-01

    The colonial ascidian Botryllus schlosseri should be considered cryptogenic (i.e., not definitively classified as either native or introduced) in the Northwest Atlantic. Although all the evidence is quite circumstantial, over the last 15 years most research groups have accepted the scenario of human-mediated dispersal and classified B. schlosseri as introduced; others have continued to consider it native or cryptogenic. We address the invasion status of this species by adding 174 sequences to the growing worldwide database for the mitochondrial gene cytochrome c oxidase subunit I (COI) and analyzing 1077 sequences to compare genetic diversity of one clade of haplotypes in the Northwest Atlantic with two hypothesized source regions (the Northeast Atlantic and Mediterranean). Our results lead us to reject the prevailing view of the directionality of transport across the Atlantic. We argue that the genetic diversity patterns at COI are far more consistent with the existence of at least one haplotype clade in the Northwest Atlantic (and possibly a second) that substantially pre-dates human colonization from Europe, with this native North American clade subsequently introduced to three sites in Northeast Atlantic and Mediterranean waters. However, we agree with past researchers that some sites in the Northwest Atlantic have more recently been invaded by alien haplotypes, so that some populations are currently composed of a mixture of native and invader haplotypes. © 2015 Marine Biological Laboratory.