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https://www.readbyqxmd.com/read/27915284/dna-extraction-protocols-may-influence-biodiversity-detected-in-the-intestinal-microbiome-a-case-study-from-wild-prussian-carp-carassius-gibelio
#1
Elena N Kashinskaya, Karl B Andree, Evgeniy P Simonov, Mikhail M Solovyev
In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTU's, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species...
December 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27915181/bioenergy-and-biodiversity-intensified-biomass-extraction-from-hedges-impairs-habitat-conditions-for-birds
#2
Ralf Sauerbrei, Birgit Aue, Christian Krippes, Eva Diehl, Volkmar Wolters
Biomass is increasingly used as an alternative source for energy in Europe. Woody material cut from hedges is considered to provide a suitable complement to maize and oilseed rape, which are currently the dominant biomass sources. Since shrubs and trees are also important habitats for birds, however, coppicing of hedges at the landscape scale may adversely affect the diversity of the avifauna. To evaluate this risk, we estimated the response of hedge birds to three management scenarios differing in cutting intensity and hedge selection...
December 1, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27914860/microplastics-ingestion-by-a-common-tropical-freshwater-fishing-resource
#3
Jacqueline Santos Silva-Cavalcanti, José Diego B Silva, Elton José de França, Maria Christina Barbosa de Araújo, Felipe Gusmão
Microplastics pollution is widespread in marine ecosystems and a major threat to biodiversity. Nevertheless, our knowledge of the impacts of microplastics in freshwater environments and biota is still very limited. The interaction of microplastics with freshwater organisms and the risks associated with the human consumption of organisms that ingested microplastics remain major knowledge gaps. In this study, we assessed the ingestion of microplastics by Hoplosternum littorale, a common freshwater fish heavily consumed by humans in semi-arid regions of South America...
November 30, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27912081/combined-effect-of-temperature-and-ammonia-on-molecular-response-and-survival-of-the-freshwater-crustacean-gammarus-pulex
#4
Y Henry, C Piscart, S Charles, H Colinet
Freshwater ecosystems are experiencing mounting pressures from agriculture, urbanization, and climate change, which could drastically impair aquatic biodiversity. As nutrient inputs increase and temperatures rise, ammonia (NH3) concentration is likely to be associated with stressful temperatures. To investigate the interaction between NH3 and temperature on aquatic invertebrate survival, we performed a factorial experiment on the survival and molecular response of Gammarus pulex, with temperature (10, 15, 20, and 25°C) and NH3 (0, 0...
November 29, 2016: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/27912020/biodiversity-increases-functional-and-compositional-resistance-but-decreases-resilience-in-phytoplankton-communities
#5
Jan M Baert, Frederik De Laender, Koen Sabbe, Colin R Janssen
There is now ample evidence that biodiversity stabilizes aggregated ecosystem functions, such as primary production, in changing environments. In primary producer systems, this stabilizing effect is found to be driven by higher functional resistance (i.e., reduced changes in functions by environmental changes) rather than through higher functional resilience (i.e., rapid recovery following environmental changes) in more diverse systems. The stability of aggregated ecosystem functions directly depends on changes in species composition and by consequence their functional contributions to ecosystem functions...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911998/tropical-forest-loss-and-its-multitrophic-effects-on-insect-herbivory
#6
José Carlos Morante-Filho, Víctor Arroyo-Rodríguez, Madelon Lohbeck, Teja Tscharntke, Deborah Faria
Forest loss threatens biodiversity, but its potential effects on multitrophic ecological interactions are poorly understood. Insect herbivory depends on complex bottom-up (e.g., resource availability and plant antiherbivore defenses) and top-down forces (e.g., abundance of predators and herbivorous), but its determinants in human-altered tropical landscapes are largely unknown. Using structural equation models, we assessed the direct and indirect effects of forest loss on insect herbivory in 40 landscapes (115 ha each) from two regions with contrasting land-use change trajectories in the Brazilian Atlantic rainforest...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911954/the-bees-among-us-modelling-occupancy-of-solitary-bees
#7
J Scott MacIvor, Laurence Packer
Occupancy modelling has received increasing attention as a tool for differentiating between true absence and non-detection in biodiversity data. This is thought to be particularly useful when a species of interest is spread out over a large area and sampling is constrained. We used occupancy modelling to estimate the probability of three phylogenetically independent pairs of native-introduced species [Megachile campanulae (Robertson)-Megachile rotundata (Fab.), Megachile pugnata Say-Megachile centuncularis (L...
2016: PloS One
https://www.readbyqxmd.com/read/27911822/urban-park-soil-microbiomes-are-a-rich-reservoir-of-natural-product-biosynthetic-diversity
#8
Zachary Charlop-Powers, Clara C Pregitzer, Christophe Lemetre, Melinda A Ternei, Jeffrey Maniko, Bradley M Hover, Paula Y Calle, Krista L McGuire, Jeanne Garbarino, Helen M Forgione, Sarah Charlop-Powers, Sean F Brady
Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911770/the-right-incentives-enable-ocean-sustainability-successes-and-provide-hope-for-the-future
#9
Jane Lubchenco, Elizabeth B Cerny-Chipman, Jessica N Reimer, Simon A Levin
Healthy ocean ecosystems are needed to sustain people and livelihoods and to achieve the United Nations Sustainable Development Goals. Using the ocean sustainably requires overcoming many formidable challenges: overfishing, climate change, ocean acidification, and pollution. Despite gloomy forecasts, there is reason for hope. New tools, practices, and partnerships are beginning to transform local fisheries, biodiversity conservation, and marine spatial planning. The challenge is to bring them to a global scale...
December 2, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27907836/implications-of-adopting-a-biodiversity-based-vulnerability-index-versus-a-shoreline-environmental-sensitivity-index-on-management-and-policy-planning-along-coastal-areas
#10
G Harik, I Alameddine, R Maroun, G Rachid, D Bruschi, D Astiaso Garcia, M El-Fadel
In this study, a multi-criteria index was developed to assess anthropogenic stressors along the Mediterranean coastline. The index aimed at geo-locating pollution hotspots for informed decision making related to coastal zone management. The index was integrated in a Geographical Information System based geodatabase implemented at several pilot areas along the Northern (Italy and France), Eastern (Lebanon), and Southern (Tunisia) Mediterranean coastlines. The generated stressor maps were coupled with a biodiversity richness index and an environmental sensitivity index to produce vulnerability maps that can form the basis for prioritizing management and mitigation interventions towards the identification of pollution hotspots and the promotion of sustainable coastal zone management...
November 28, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27907260/ten-year-responses-of-ground-dwelling-spiders-to-retention-harvest-in-the-boreal-forest
#11
Jaime Pinzon, John R Spence, David W Langor, David P Shorthouse
The Ecosystem Management Emulating Natural Disturbances (EMEND) project tests the hypothesis that varying levels of green tree retention maintain and retain forest biodiversity better than conventional clear-cutting. We studied epigaeic spiders to assess biodiversity changes 2, 5, and 10 yr following a range of partial retention harvests (clear-cut, 10-75% retention) and unharvested controls in four boreal mixedwood cover types. A total of 56 371 adult spiders representing 220 species was collected using pitfall traps...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907259/spectral-diversity-area-relationships-for-assessing-biodiversity-in-a%C3%A2-wildland-agriculture-matrix
#12
Kyla Marie Dahlin
Species-area relationships have long been used to assess patterns of species diversity across scales. Here, this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum; one set of well-mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three principal component values and the principal components' convex hull volume, spectral diversity was compared within and among these plots and to null expectations for perfectly random and perfectly patchy landscapes...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907252/residential-yards-as-designer-ecosystems-effects-of-yard%C3%A2-management-on-land-snail-species-composition
#13
Elizabeth A Bergey, Laura L Figueroa
Residential yards comprise the majority of green space in urban landscapes, yet are an understudied system because of access issues and because yards may be considered biologically depauperate. Yards are purposely created and managed and, hence, qualify as designer ecosystems, a term borrowed from restoration ecology. We investigated whether yard management (watering regime, mulching, and chemical use) or dog presence affected land snail assemblage composition and described the pattern of native vs. nonnative species among yards...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907121/environmental-and-geographical-factors-structure-soil-microbial-diversity-in-new-caledonian-ultramafic-substrates-a-metagenomic-approach
#14
Véronique Gourmelon, Laurent Maggia, Jeff R Powell, Sarah Gigante, Sara Hortal, Claire Gueunier, Kelly Letellier, Fabian Carriconde
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity...
2016: PloS One
https://www.readbyqxmd.com/read/27907117/the-composition-and-spatial-patterns-of-bacterial-virulence-factors-and-antibiotic-resistance-genes-in-19-wastewater-treatment-plants
#15
Bing Zhang, Yu Xia, Xianghua Wen, Xiaohui Wang, Yunfeng Yang, Jizhong Zhou, Yu Zhang
Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4...
2016: PloS One
https://www.readbyqxmd.com/read/27905931/a-temporal-assessment-of-nematode-community-structure-and-diversity-in-the-rhizosphere-of-cisgenic-phytophthora-infestans-resistant-potatoes
#16
Vilma Ortiz, Sinead Phelan, Ewen Mullins
BACKGROUND: Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a 'barometer' of a soil's functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere...
December 1, 2016: BMC Ecology
https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#17
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27902440/synechococcus-diversity-along-a-trophic-gradient-in-the-osterseen-lake-district-bavaria
#18
Joachim Ruber, Franziska Bauer, Andrew Millard, Uta Raeder, Jürgen Geist, Katrin Zwirglmaier
Picocyanobacteria are important primary producers in freshwater, however there is still a knowledge gap regarding their diversity at the strain level. For this reason, the microbial diversity of four lakes with different trophic states was investigated by sequencing of the 16S rRNA gene using universal primers. The study was performed in selected lakes of the Osterseen Lake District, Germany, from 2012 to 2014 (Lake Schiffhuettensee: eutrophic; Lake Ostersee: meso-oligotrophic; Lake Groebensee: oligotrophic; Lake Lustsee: oligotrophic)...
November 1, 2016: Microbiology
https://www.readbyqxmd.com/read/27901123/hill-number-as-a-bacterial-diversity-measure-framework-with-high-throughput-sequence-data
#19
Sanghoon Kang, Jorge L M Rodrigues, Justin P Ng, Terry J Gentry
Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (Na), to control the variability associated with rare taxa by differentially weighing them...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900850/hybridization-between-pollination-syndromes-as-an-ecological-and-evolutionary-resource
#20
Quentin Cronk, Ji Yong Yang
In plants, pollination syndromes (the correlated presence of many features of relevance to pollination mode, for instance pollination by a particular animal clade) are a striking feature of plant biodiversity, providing great floral phenotypic diversity (Fenster et al. ). Adaptation to a particular animal pollinator provides an explanation for why recently diverged plants can have such extreme differentiation in floral form. One might expect such elaborate adaptations to provide a high degree of pollinator specificity and hence reproductive isolation, but there are many cases where substantial gene flow exists between extreme floral morphs (see Table 1), and the resulting hybrids may be highly fertile...
December 2016: Molecular Ecology
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