scholarly journals Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

2021 ◽  
Author(s):  
Sven Weber ◽  
Lukas Brink ◽  
Manuel Wörner ◽  
Sven Künzel ◽  
Michael Veith ◽  
...  
Keyword(s):  
Food Web ◽  
Water Samples ◽  
Large Scale ◽  
Ecological Impact ◽  
Diet Analysis ◽  
Alternative Source ◽  
Dietary Analysis ◽  
Alpha And Beta Diversity ◽  
Invasive Bivalves ◽  
Primer Sets

AbstractMolecular gut content analysis is a popular tool to study food web interactions and was recently also suggested as an alternative source for DNA based biomonitoring. However, the overabundant consumer’s DNA often outcompetes that of its diet during PCR. Blocking approaches are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. We here designed an assay to monitor the eukaryotic diet of mussels and test their utility as biological eDNA filters to monitor planktonic communities. We designed several rDNA primer sets with a broad taxonomic suitability for eukaryotes, which suppress the amplification of mussels. The primers were tested using mussel DNA extracts and the results were compared to eDNA water samples collected next to the mussel colonies. Taxonomic recovery, as well as patterns of alpha and beta diversity, were compared between mussels and water samples. In addition, we analyzed time series samples of mussel samples from different German rivers. Our primer sets efficiently block the amplification of various mussel genera. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also recover various taxa of possible commensals and parasites, associated with the mussels. Our protocol will enable large scale dietary analysis in mussels, facilitate aquatic food web analysis, elucidate the ecological impact of invasive bivalves and the rapid survey of mussel aquacultures for pathogens. Moreover, we show that mussels could serve as an interesting complementary DNA source for biomonitoring.

scholarly journals Fencing affects African wild dog movement patterns and population dynamics

Oryx ◽  
2021 ◽  
pp. 1-9
Author(s):  
Helen M. K. O'Neill ◽  
Sarah M. Durant ◽  
Stefanie Strebel ◽  
Rosie Woodroffe
Keyword(s):  
Population Dynamics ◽  
Large Scale ◽  
Animal Movement ◽  
Landscape Connectivity ◽  
Ecological Impact ◽  
Movement Patterns ◽  
Wrong Side ◽  
African Wild Dog ◽  
Wild Dog ◽  
Wild Dogs

Abstract Wildlife fences are often considered an important tool in conservation. Fences are used in attempts to prevent human–wildlife conflict and reduce poaching, despite known negative impacts on landscape connectivity and animal movement patterns. Such impacts are likely to be particularly important for wide-ranging species, such as the African wild dog Lycaon pictus, which requires large areas of continuous habitat to fulfil its resource requirements. Laikipia County in northern Kenya is an important area for wild dogs but new wildlife fences are increasingly being built in this ecosystem. Using a long-term dataset from the area's free-ranging wild dog population, we evaluated the effect of wildlife fence structure on the ability of wild dogs to cross them. The extent to which fences impeded wild dog movement differed between fence designs, although individuals crossed fences of all types. Purpose-built fence gaps increased passage through relatively impermeable fences. Nevertheless, low fence permeability can lead to packs, or parts of packs, becoming trapped on the wrong side of a fence, with consequences for population dynamics. Careful evaluation should be given to the necessity of erecting fences; ecological impact assessments should incorporate evaluation of impacts on animal movement patterns and should be undertaken for all large-scale fencing interventions. Where fencing is unavoidable, projects should use the most permeable fencing structures possible, both in the design of the fence and including as many purpose-built gaps as possible, to minimize impacts on wide-ranging wildlife.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

Detecting predation of a burrow-nesting seabird by two introduced predators, using stable isotopes, dietary analysis and experimental removals

2007 ◽  
Vol 34 (6) ◽  
pp. 443 ◽  
Author(s):  
Grant A. Harper
Keyword(s):  
Rattus Rattus ◽  
Isotopic Analysis ◽  
Diet Analysis ◽  
Passerine Birds ◽  
Dietary Analysis ◽  
Stable Isotopic Analysis ◽  
Introduced Predators ◽  
Ship Rat ◽  
Stable Isotopic ◽  
Burrowing Seabirds

Burrowing seabirds are vulnerable to extirpation by introduced predators such as rats, but much evidence of predation is circumstantial. On Taukihepa, an island off southern New Zealand, two possible predators exist with sooty shearwaters (Puffinus griseus): the weka (Gallirallus australis), a large rail, and the ship rat (Rattus rattus), both introduced to the island. It was expected that chick predation would be principally by weka, the much larger of the two predators. To measure losses of sooty shearwater chicks to weka or rats, nests were monitored with burrow-scopes at six sites in the summers of 2003–04 and 2004–05. In three of the sites rats were removed on 4-ha grids by trapping. In the other three sites rats were not trapped. In addition, weka were removed from all six sites in 2005. Concurrent diet analysis of weka and rat stomachs was undertaken as well as stable isotopic analysis (δ13C, δ15N) of samples from rats and weka. These were compared with possible prey items including sooty shearwaters. Additional stable isotope samples were taken from Pacific rats (Rattus exulans), a small rat species present with weka and sooty shearwaters on nearby Moginui Island. Weka diet comprised ~40% of bird remains by volume and calculations using Isosource, an isotopic source portioning model, estimated sooty shearwaters contributed 59% (range: 15–71%) of weka diet during the sooty shearwater chick-raising period. Ship rats, in contrast, had very depleted δ13C isotope signatures compared with sooty shearwaters and bird remains contributed <9% of diet by volume, with Isosource calculations suggesting that ship rats consumed more passerine birds (mean: 30%; range 5–51%) than sooty shearwaters (mean 24%; range: 0–44%). In both summers, more chicks were lost on sites from which rats had been removed than on control sites. When weka were removed in 2005, fewer chicks were lost than in 2004 and significantly fewer weka-killed chicks were found on weka-removal sites than on non-removal sites. Weka were the principal predator of sooty shearwater chicks, depredating an estimated 9.9% of nests. Combining several techniques quantified the loss and identified the principal predator of a seabird in decline.

scholarly journals Physiochemical and Microbiological Analysis of Drinking Water in Chattogram City, Bangladesh

2020 ◽  
pp. 42-50
Author(s):  
Kanij Fatema Nishan ◽  
Nilufa Yeasmin ◽  
Urmi Rani Devi ◽  
Sumiya Akter ◽  
Md. Abu Bakar ◽  
...  
Keyword(s):  
Water Quality ◽  
Drinking Water ◽  
Water Samples ◽  
Total Coliform ◽  
Drinking Water Quality ◽  
Sampling Location ◽  
Microbiological Analysis ◽  
Alternative Source ◽  
Safe Alternative ◽  
Total Dissolved Solid

Chattogram is the second most populated city in Bangladesh. This port city faces a serious threat mainly due to the lack of safe drinking water. This study was conducted for determining drinking water quality of groundwater sources in Chattogram city. The study was performed in the BCSIR laboratory, Chattogram. It was carried out for a period of six months from 1st July, 2018 to 31th December, 2018. Total six water samples were collected from three different locations (Baluchora, C&B colony and Khulshi area). Each sampling location consists of two separate sampling points. Physicochemical parameters of the collected samples like Temperature, pH, Electrical Conductivity (EC), Total dissolved solid (TDS), Hardness, Turbidity and concentration of Cl, As, Mn, Fe, Pb, Cr and Cd were examined. Microbial parameters like Total Coliform (TC) were also measured. All the analyzed parameters compared with BSTI and WHO drinking water quality standards to understand the overall ground water quality status of the study area. The results reveal that water samples in almost all locations were contaminated with microbial contamination and that the range of physico-chemical parameters was not adequate for consumption. Preliminary treatments like boiling, filtering etc are required before using groundwater for drinking and the necessary measures must be taken for a safe alternative source of drinking water.

scholarly journals Micropropagation of Tarenaya rosea (Cleomaceae) from leaf explants

Rodriguésia ◽  
2021 ◽  
Vol 72 ◽  
Author(s):  
Claudia Simões-Gurgel ◽  
Tatiana Carvalho de Castro ◽  
Cátia Henriques Callado ◽  
Lívia da Silva Cordeiro ◽  
Norma Albarello
Keyword(s):  
Large Scale ◽  
Plant Conservation ◽  
Leaf Explants ◽  
Plant Production ◽  
Anthocyanin Content ◽  
Alternative Source ◽  
Regeneration Rate ◽  
Culture Techniques ◽  
Regenerated Plants

Abstract In vitro culture techniques are recognized as efficient strategies for large-scale plant production, as well as providing alternatives for plant conservation. In this study the micropropagation of Tarenaya rosea was established using petiole and foliar blade segments cultivated on MS medium with 6-benzyladenine (BA) and/or 6-furfurylaminopurine (KIN). The regeneration rate from explants was evaluated after 30-days in culture, as well as the proliferation rate from explant-derived shoots, reached after four subcultures performed at 30-days in culture. In vitro propagation occurred by both direct (DO) and indirect (IO) organogenesis. The highest regeneration rates by DO (50% to 100%) were reached on media containing only BA, while morphogenic calluses (IO) were mainly formed with BA+KIN. Explants on media with BA showed the presence of small black nodules on their surface, and histological analysis revealed the presence of trichomes with anthocyanin content. Elongation and rooting were reached on growth regulator-free MS. Acclimatization rates around 80% were achieved and the in vitro-regenerated plants were successfully maintained under field conditions. Results show significant morphogenetic potential of T. rosea from leaf explants, mainly when cultivated in the presence of 4.4 µM BA, providing a new alternative source of plant material for biotechnological and in vitro conservation studies.

scholarly journals A Simple Technique for the Identification of Environmental DNA (eDNA ) in the Water Samples

2021 ◽  
pp. 77-80
Author(s):  
Chitra K. Y.
Keyword(s):  
Water Samples ◽  
Large Scale ◽  
Dna Isolation ◽  
Simple Technique ◽  
Environmental Dna ◽  
Water Bodies ◽  
Easy Method ◽  
Selective Staining ◽  
Generation Sequencing ◽  
Dark Pink

The environmental DNA(eDNA) is the DNA that is shed by the organisms in their environment by different ways viz. , mucous, faeces, skin, eggs, sperms and also when these organisms die due to natural death or disease. The eDNA will persist for several days. Identification of eDNA is a useful method of determining the organisms present in an aquatic environment like amphibians, reptiles, fishes , insects and larval forms of some of these organisms. By analysing the e-DNA it is possible to monitor the species distribution in water bodies like lakes and ponds simply by collecting a sample of water. The technique can be applied for the survey of the water bodies on a large scale for the genomic, taxonomic as well as pollutional studies. The DNA isolation procedures that are available are laborious and time consuming. Therefore, during the present study, a simplified method was devised i. e. , isolation of eDNA with ethanol after which Feulgen stain was applied to identify and confirm it, as it is an easy method before proceeding to work with the isolated eDNA using other techniqnies for further studies. The Feulgen method is used for the selective staining and the localisation of the DNA in the tissues but is adopted during the present study for the water samples for quick identification of eDNA. The smear of eDNA stained with Feulgen showed dark pink or magenta colour under the microscope where it was concentrated but stained lightly when dispersed and fragmented as observed in the present study. Further studies of the isolated eDNA are in progress in our laboratory for quantifying and sequencing eDNA using latest techniques like next generation sequencing for the identification of fish species in the lakes.

scholarly journals Ecological impact and spread of an invasive paper wasp in New Zealand (Hymenoptera: Vespidae)

2021 ◽  
Author(s):  
Matthew Howse
Keyword(s):  
At Risk ◽  
Invasive Species ◽  
New Zealand ◽  
Ecological Impact ◽  
Diet Analysis ◽  
Paper Wasp ◽  
Gut Contents ◽  
Suitable Habitat ◽  
The South ◽  
The North

<p><b>Social wasps are considered among the most successful and impactful invasive species in the world. One species, Polistes dominula has spread from its native Mediterranean range to every continent except Antarctica. This wasp reached New Zealand in the last decade where it has established in the north of the South Island, however, reports of its presence are increasing throughout the country. Due to its recent arrival in New Zealand, little is known about where this species is likely to establish or what impacts it may have on local insect communities. In this thesis, I conducted two studies to investigate these questions, providing valuable information that may inform future management of this invasive species. </b></p><p>In chapter 2, I used two bioclimatic modelling methods to predict areas of suitable habitat across four regions in the southern hemisphere. These models were informed by global temperature and precipitation data as well as global distribution occurrence data of P. dominula. These data were used to estimate conditions most highly correlated with the presence of this wasp. The models identified large areas across the target regions that were climatically suitable for the establishment of P. dominula. Many of these areas are not known to currently contain populations of this species, representing habitat potentially vulnerable to further invasion by P. dominula. Areas across South America, South Africa and Australia were predicted to be climatically suitable. In New Zealand, much of the North Island and eastern parts of the South Island were predicted to be suitable habitat for this wasp. These results suggest that P. dominula could potentially establish across more of the country and expand its invaded range. Information provided by these models may guide conservation and biosecurity management by highlighting key areas where prevention and mitigation should be prioritized. </p><p>In chapter 3, I used molecular diet analysis to investigate the range of prey being utilised by P. dominula in New Zealand. Using DNA barcoding, larval gut contents of P. dominula and another closely related species, Polistes chinensis, were analysed to identify what species were present in the diet of both wasps. Butterflies and moths (Lepidoptera) were found to be the most highly represented order in both species’ diets. True bugs (Hemiptera) and flies (Diptera) were also abundant. Both wasps were shown to consume a range of native and introduced species including a number of agricultural pests. P. dominula was found to utilise a wider range of prey than P. chinensis. This more diverse prey range, combined with known differences in nesting behaviour, suggest that P. dominula may represent a more significant threat to invertebrate diversity than the already well-established P. chinensis. These results may inform conservation and biosecurity managers on which species are most at risk where this new invasive wasp becomes established. </p><p>This thesis provides insights into the potential impacts of a new invasive species to New Zealand. Both chapters represent the first time that these methods have been used to study P. dominula. This work highlights the need for continued monitoring of wasp populations throughout New Zealand, especially in regions highlighted as vulnerable to P. dominula establishment. We also suggest the need to prioritise the conservation of ‘at-risk’ species in coastal and human-altered habitats. Increased public engagement through the citizen-science initiatives should be encouraged while more research into management and control methods is recommended.</p>

scholarly journals Molecular Verification of Bloom-forming Aphanizomenon flos-aquae and Their Secondary Metabolites in the Nakdong River

2018 ◽  
Vol 15 (8) ◽  
pp. 1739 ◽  
Author(s):  
Hae-Kyung Park ◽  
Mi-Ae Kwon ◽  
Hae-Jin Lee ◽  
Jonghee Oh ◽  
Su-Heon Lee ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Water Samples ◽  
Its Region ◽  
Cyanobacterial Blooms ◽  
Specific Primer ◽  
Nakdong River ◽  
Off Flavors ◽  
Primer Sets ◽  
The Nakdong River ◽  
Harmful Cyanobacterial Blooms

Aphanizomenon spp. have formed harmful cyanobacterial blooms in the Nakdong River during spring, autumn, and now in winter, and the expansion of blooming period and area, associated with the global warming is predicted. The genus Aphanizomenon has been described to produce harmful secondary metabolites such as off-flavors and cyanotoxins. Therefore, the production of harmful secondary metabolites from the Aphanizomenon blooms in the Nakdong River needs to be monitored to minimize the risk to both water quality and public health. Here, we sampled the cyanobacterial blooms in the Nakdong River and isolated ten Aphanizomenon strains, morphologically classified as Aphanizomenon flos-aquae Ralfs ex Bornet et Flahault 1888. Phylogenetic analysis using 16S rRNA and internal transcribed spacer (ITS) region nucleotide sequences confirmed this classification. We further verified the harmful secondary metabolites-producing potential of A. flos-aquae isolates and water samples containing cyanobacterial blooms using PCR with specific primer sets for genes involved in biosynthesis of off-flavor metabolites (geosmin) and toxins (microcystins, saxitoxins and cylindrospermopsins). It was confirmed that these metabolite biosynthesis genes were not identified in all isolates and water samples containing only Aphanizomenon spp. Thus, it is likely that there is a low potential for the production of off-flavor metabolites and cyanotoxins in Aphanizomenon blooms in the Nakdong River.

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