Academic literature on the topic 'Taxonomic treatments'
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Journal articles on the topic "Taxonomic treatments"
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Hupperts, Stefan F., Christopher R. Webster, Robert E. Froese, Erik A. Lilleskov, Amy M. Marcarelli, and Yvette L. Dickinson. "Increasing ground-layer plant taxonomic diversity masks declining phylogenetic diversity along a silvicultural disturbance gradient." Canadian Journal of Forest Research 50, no. 12 (December 2020): 1259–67. http://dx.doi.org/10.1139/cjfr-2020-0055.
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Most plant diversity in temperate deciduous forests is found in the ground layer, but nearly all studies comparing plant community assembly using taxonomic, trait, and phylogenetic diversity indices are limited to woody plants. To examine the relationship between short-term ground-layer plant community assembly and disturbance severity, we leveraged a silvicultural experiment that applied a combination of harvest and site preparation treatments in a northern hardwood forest in Michigan, USA. We predicted that after two growing seasons, plant communities would be less sensitive to harvest treatments when compared with site preparation treatments that disturb the rhizosphere and modify rooting substrate. We also predicted that an increase in taxonomic diversity would accompany a decline in trait diversity and phylogenetic diversity. Instead, plant species composition responded similarly to harvest treatment and site preparation treatment. However, our measure of disturbance severity was positively correlated with both trait diversity and taxonomic diversity but negatively correlated with phylogenetic diversity, indicating that increasingly diverse traits and taxonomies along this disturbance severity gradient were comprised of more phylogenetically simple plant communities. Informed management decisions should therefore consider the underlying value of each diversity measure, as taxonomic diversity alone may not be the best metric for assessing plant community assembly.
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Pal, Himani, and Manabendra Dutta Choudhury. "Cyperaceae: A Review of its Taxonomic Treatments." Pleione 11, no. 2 (December 31, 2017): 195. http://dx.doi.org/10.26679/pleione.11.2.2017.195-207.
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Whittemore, Alan T. "A simple method for computerizing taxonomic treatments." TAXON 45, no. 3 (August 1996): 503–11. http://dx.doi.org/10.2307/1224142.
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Serrano, Miguel, Lyuboslava Dimitrova, and Santiago Ortiz. "Nomenclature and Typification of the Jasione L. (Campanulaceae) Groups from the Eastern Mediterranean Basin." Plants 13, no. 1 (December 22, 2023): 50. http://dx.doi.org/10.3390/plants13010050.
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In this research, all the published names of Jasione (Campanulaceae) in the species, subspecies, and variety ranks for populations from the Balkan and Anatolian peninsulas are reviewed, including names of taxa allied to these groups in surrounding areas. These two areas are among the main centers of diversity of the genus, albeit no recent revisions to address the regional taxonomical complexity of the genus have been published for the Balkans and Anatolia. In this work, the taxonomic status and typification of twenty-six published names are discussed, including the plethora of names within the Jasione heldreichii, J. supina, and J. orbiculata taxonomic complexes. In total, eleven lectotypes and one neotype are designated for names from the aforementioned regions, plus one from southern Italy. This nomenclatural clarification establishes a reference for ongoing and future taxonomic and evolutionary studies of Jasione in the Mediterranean basin. In a genus prone to micro-endemism and cryptospeciation, a number of the historically described forms, despite being disregarded by current taxonomic treatments, may, therefore, deserve further attention.
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GUIDOTI, MARCUS, FELIPE LORENZ SIMÕES, TATIANA PETERSEN RUSCHEL, VALDENAR DA ROSA GONÇALVES, CAROLINA SOKOLOWICZ, and DONAT AGOSTI. "Using taxonomic treatments to assess an author’s career: the impactful Jocélia Grazia." Zootaxa 4958, no. 1 (April 14, 2021): 12–33. http://dx.doi.org/10.11646/zootaxa.4958.1.4.
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Here we present a descriptive analysis of the bibliographic production of the world-renowned heteropterist Dr. Jocélia Grazia and comments on her taxonomic reach based on extracted taxonomic treatments. We analyzed a total of 219 published documents, including scientific papers, scientific notes, and book chapters. Additionally, we applied the Plazi workflow to extract taxonomic treatments, images, tables, treatment citations and materials citations, and references from 75 different documents in accordance with the FAIR (Findability, Accessibility, Interoperability, and Reuse) principles and made them available on the Biodiversity Literature Repository (BLR), hosted on Zenodo, and on TreatmentBank. We found that Dr. Grazia published 200 new names, including species (183) and genera (17), and 1,444 taxonomic treatments in total. From these, 104 and 581, respectively, were extracted after applying the Plazi Workflow. A total of 544 figures, 50 tables, 2,242 references, 2,107 materials citations, and 1,101 treatment citations were also extracted. In order to make her publications properly citable and accessible, we assigned DOIs (Digital Object Identifiers) for all publications that lacked this persistent identifier, including those that were not processed (88 in total), therefore enhancing the open-access share of her publications.
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WANG, LISONG, HONGRUI ZHANG, MARK F. WATSON, and SANDRA KNAPP. "On the identity of Sium frigidum (Apiaceae)." Phytotaxa 288, no. 3 (December 16, 2016): 265. http://dx.doi.org/10.11646/phytotaxa.288.3.7.
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Taxonomic identity of Sium frigidum remains confusing; the taxon has been treated as belonging to four different genera including Apium, Sium, Chamaesium and Sinocarum. After field investigation, detailed examination of herbarium specimens, and analyses of molecular data, the results show that S. frigidum represent plants only known from southwest China, and conspecific with Apium ventricosum. Therefore, a new combination name, Sium ventricosum, is proposed with full taxonomic treatments. Taxonomic confusing related with this species is also discussed.
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YANG, YE-KUN, QIONG ZHANG, JIN-LIN MA, and SHI-XIONG YANG. "Taxonomic treatments of Pyrenaria jonquieriana (Theaceae) and related taxa." Phytotaxa 525, no. 3 (November 19, 2021): 237–42. http://dx.doi.org/10.11646/phytotaxa.525.3.6.
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On the basis of field investigation and herbarium specimen examination, Tutcheria multisepala, Pyrenaria poilaneana, Parapyrenaria indochinensis and Camellia luuana are treated to the synonymy of Pyrenaria jonquieriana. In addition, lectotypes are designated for the names Pyrenaria jonquieriana and Pyrenaria poilaneana.
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Peterson, A. Townsend, and Adolfo G. Navarro-Sigüenza. "Consistency of Taxonomic Treatments: A Response to Remsen (2005)." Auk 123, no. 3 (2006): 885. http://dx.doi.org/10.1642/0004-8038(2006)123[885:cottar]2.0.co;2.
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Peterson, A. Townsend, and Adolfo G. Navarro-Sigüenza. "Consistency of Taxonomic Treatments: A Response to Remsen (2005)." Auk 123, no. 3 (July 1, 2006): 885–87. http://dx.doi.org/10.1093/auk/123.3.885.
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YANG, DONGMEI, JIAMEI WANG, RUI GUO, HONGJUAN ZHU, CHANGWANG MA, JING YU, YA LIU, YOUGEN WU, and HUI SHANG. "New taxonomic treatments in the Pteris fauriei group (Pteridaceae)." Phytotaxa 647, no. 3 (May 14, 2024): 223–36. http://dx.doi.org/10.11646/phytotaxa.647.3.2.
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The dividing lines between species in the Pteris fauriei group (Pteridaceae) are questionable and the systematic positions of some species in this group remain unclear. To help comprehensively understand the phylogenetic relationships and resolve the taxonomic problems in this group a phylogenetic tree was reconstructed based on five chloroplast DNA regions (atpA, matK, rbcL, rps4-trnS & trnL-trnF) from 22 Pteris taxa. Additionally, their spore morphology and type materials were studied. Based on the molecular and morphology evidence, we made treatments as follow: P. oshimensis Hieron. var. paraemeiensis Ching ex Ching et S.H. Wu was raised as a species from a variety of P. oshimensis Hieron; P. fauriei Hieron. var. chinensis Ching et S.H. Wu was treated as a synonym of P. austrotaiwanensis Y.S. Chao, rather than a synonym of P. latipinna Y.S. Chao & W.L. Chiou; and P. omeiensis Ching was restored to species status from a synonym of P. oshimensis Hieron.
Dissertations / Theses on the topic "Taxonomic treatments"
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Mondal, Sujit. "Taxonomy, phenology and ethnobotany of palms in West Bengal." Thesis, University of North Bengal, 2019. http://ir.nbu.ac.in/handle/123456789/4044.
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Shkwa, Essokne Rafaa A. "Taxonomic treatment of the genus Adenocarpus (Leguminosae)." Thesis, University of Reading, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.553138.
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The variation in the genus Adenocarpus DC. (Leguminosae) was sampled as far as possible from its complete distribution range, the Mediterranean and tropical African regions. Characters for taxonomy were obtained from morphology and phytochemistry; a DNA analysis was also undertaken. A detailed study of morphological characters was undertaken and analyzed by one-way ANOVA, discriminant analysis and Cross Tabulation with Chi square. A flavonoid and isoflavonoid survey to provide new taxonomic characters was made using high performance liquid chromatography with diode array detection and atmospheric pressure chemical ionization-mass spectrometry. For ten of these variants, 2-8 samples were examined to investigate flavonoid variation. Nineteen flavonoids belonging to five classes (flavone C- and O-glycosides, flavonol glycosides, isoflavone glycosides and flavanones) were detected. The nuclear ITS and chloroplast trnL-trnF DNA were sequenced to provide the relationships among the variants of Adenocarpus. The phylogenies obtained from both individual and the combined analyses of the data sets were congruent. A good correlation was found in that each of the molecular clades could also be characterised by a combination of flavonoids. For example, the species in clade 4, which are distributed in South and South-East Europe and tropical Africa, are characterised by the presence of flavonol O-glycosides and 5-hydroxyisoflavone O-glycosides. In contrast, flavonol O-glycosides were absent from all but one species of the other three clades, which have a mainly North Africa distribution, and these species produce flavone mono- C-glycosides and/or flavone 7-0-glycosides instead. In addition flavone 41-O-glycosides were only found in species of clade 1 and flavanones were mainly restricted to clade 3. However, the results from the morphology, phytochemistry and phylogeny provided a framework that has been used as a basis for a new classification of the genus. Twenty- four species, including a new species from the Middle Atlas of Morocco, three subspecies and one variety of the genus Adenocarpus (Leguminosae) are recognized in a new systematic account.
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Tea, Yi Kai. "Evolution on coral reefs, with systematic treatments of the pencil and fairy wrasses (Teleostei: Labridae: Pseudojuloides & Cirrhilabrus)." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/29726.
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Fishes represent half of all of the living species of vertebrates that have been described to date. Most species of fish are marine, with at least a third found exclusively in coral reefs. Yet the phylogenetic relationships of coral reef fishes and the drivers of their diversification remain poorly understood, particularly for taxonomic groups at the incipient stages of speciation. Despite the increasing application of high-throughput sequencing techniques to other taxonomic groups, much of the research conducted on coral reef fishes still relies on more traditional sources of information, such as morphology and mitochondrial sequence data. These methods are unreliable in resolving taxonomically problematic groups such as the Labridae, where many groups are still rapidly radiating, and the processes driving this are not well understood. It is therefore prudent to use a combined, integrative approach using both morphological and high-throughput sequencing techniques. This thesis uses the aforementioned techniques, integrated with morphological studies, to tease apart the relationships for members of the Labridae, in particular the fairy and pencil wrasses (Cirrhilabrus and Pseudojuloides respectively). Additionally, it includes taxonomic descriptions of eight new species, as well as investigations into general themes on coral reefs, including, but not limited to hybridisation, deep reef communities, and historical biogeography.
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Coco, Joseph. "PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/1297.
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RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing technologies [1]. A plethora of tools have been developed to analyze and visualize the transcriptome data from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] [3]. This allows for analysis of most reads produced by the experiments, but these tools typically discard reads that do not match well with the reference genome. This additional information could reveal important insight into the experiment and possible contributing factors to the condition under consideration. We introduce PARSES, a pipeline constructed from existing sequence analysis tools, which allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition.
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Paladini, Giuseppe. "Aspects of systematics and host specificity for Gyrodactylus species in aquaculture." Thesis, University of Stirling, 2012. http://hdl.handle.net/1893/17043.
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Of the 430+ extant species of Gyrodactylus, ectoparasitic monogenetic flukes of aquatic vertebrates, Gyrodactylus salaris Malmberg, 1957 is arguably the most well-known. Following the introduction of this species into Norway in the 1970s with consignments of infected Atlantic salmon smolts, Salmo salar L., this species has had a devastating impact on the Norwegian Atlantic salmon population, decimating wild stocks in over 40 rivers. Gyrodactylus salaris is the only OIE (Office International des Epizooties) listed parasitic pathogen of fish and has been reported from 19 countries across Europe, though many of these records require confirmation. The UK, Ireland and some selected watersheds in Finland are currently recognised as G. salaris-free states; however, the threat that this notifiable parasite poses to the salmon industry in the UK and Ireland is of national concern. Current British contingency plans are based on the assumption that if G. salaris were to be introduced, the parasite would follow similar dynamics to those on salmonid stocks from across Scandinavia, i.e. that Atlantic strains of Atlantic salmon would be highly susceptible to infection, with mortalities resulting; that brown trout, Salmo trutta fario L., would be resistant and would lose their infection in a relatively short period of time; and that grayling, Thymallus thymallus (L.), would also be resistant to infection, but would carry parasites, at a low level, for up to 143 days. Two of the objectives of this study were to confirm the current distribution of G. salaris across Europe, and then, to investigate the relative susceptibility of British salmonids to G. salaris, to determine whether they would follow a similar pattern of infection to their Scandinavian counterparts or whether, given their isolation since the last glaciation and potential genetic differences, they would exhibit different responses. It has been almost six years since the distribution of G. salaris across Europe was last evaluated. Some of the European states identified as being G. salaris-positive, however, are ascribed this status based on misidentifications, on partial data resulting from either morphological or molecular tests, or according to records that have not been revisited. Additional Gyrodactylus material from selected salmonids was obtained from several countries to contribute to current understanding regarding the distribution of G. salaris across Europe. From the work conducted in the study, G. salaris is reported from Italy for the first time, alongside three other species, and appears to occur extensively throughout the central region without causing significant mortalities to their rainbow trout, Oncorhynchus mykiss (Walbaum), hosts. The analysis of archive material from G. salaris-positive farms would suggest that G. salaris has been in the country for at least 12 years. Material obtained from rainbow trout from Finland and Germany was confirmed as G. salaris supporting existing data for these countries. No specimens of G. salaris, however, were found in the additional Gyrodactylus material obtained from Portuguese and Spanish rainbow trout, only Gyrodactylus teuchis Lautraite, Blanc, Thiery, Daniel et Vigneulle, 1999, a morphologically similar species was found. Gyrodactylus salaris is now reported from 23 out of ~50 recognised states throughout Europe, only 17 of these however, have been confirmed by either morphology or by an appropriate molecular test, and only ten of these records have been confirmed by a combination of both methods. To assess the susceptibility of English and Welsh salmonids to G. salaris, a number of salmonid stocks of wild origin, were flown to the Norwegian Veterinary Institute (NVI) in Oslo, where they were experimentally challenged with G. salaris. Atlantic salmon from the Welsh River Dee, S. trutta fario from the English River Tyne and T. thymallus from the English River Nidd, raised from wild stock in government hatcheries, were flown out and subsequently challenged with G. salaris haplotype A. After acclimation, each fish was infected with ~50–70 G. salaris and marked, so that parasite numbers on individual fish could be followed. The dynamics on individual fish were followed against a control (Lierelva Atlantic salmon). The experiment found that the number of G. salaris on S. salar from the River Dee continued to rise exponentially to a mean intensity (m.i.) of ~3851 G. salaris fish-1 (day 40 post-infection). These salmon were highly susceptible, more so than the Norwegian salmon control (m.i. ~1989 G. salaris fish-1 d40 post-infection) and were unable to regulate parasite numbers. The S. trutta fario and T. thymallus populations, although initially susceptible, were able to control and reduce parasite burdens after 12 (m.i. ~146 G. salaris fish-1) and 19 (m.i. ~253 G. salaris fish-1) days, respectively when peak infections were seen. Although the latter two hosts were able to limit their G. salaris numbers, both hosts carried infections for up to 110 days (i.e. when the experiment was terminated). The ability of S. trutta fario and T. thymallus to carry an infection for long periods increases the window of exposure and the potential transfer of G. salaris to other susceptible hosts. The potential role that brown trout may play in the transmission and spread of G. salaris in the event of an outbreak, needs to be considered carefully, as well as the interpretation of the term “resistant” which is commonly used when referring to brown trout’s susceptibility to G. salaris. The current British surveillance programmes for G. salaris are focused on the screening of Atlantic salmon and on the monitoring of the rainbow trout movements. The findings from this study demonstrate that G. salaris can persist on brown trout for long periods, and suggest that brown trout sites which overlap with Atlantic salmon or rainbow trout sites are also included within surveillance programmes and that the role that brown trout could play in disseminating infections needs to be factored into contingency/management plans. Throughout the course of the study, a number of parasite samples were sent to the Aquatic Parasitology Laboratory at Stirling for evaluation. Some of these samples represented Gyrodactylus material that were associated with fish mortalities, but the species of Gyrodactylus responsible appeared to be new to science. A further aspect of this study was, therefore, to investigate these Gyrodactylus related mortalities in aquaculture stock and to describe the species found in each case, which may represent emerging pathogens. The two new species, Gyrodactylus orecchiae Paladini, Cable, Fioravanti, Faria, Di Cave et Shinn, 2009 and Gyrodactylus longipes Paladini, Hansen, Fioravanti et Shinn, 2011 on farmed gilthead seabream, Sparus aurata L., were collected from several Mediterranean farms. The finding of G. orecchiae in Albania and Croatia was associated with 2–10% mortality of juvenile stock and represents the first species of Gyrodactylus to be formally described from S. aurata. Subsequently, G. longipes was found in Bosnia-Herzegovina and Italy, and at the Italian farm site, it occurred as a mixed infection with G. orecchiae, but these infections did not appear to result in any loss of stock. Unconfirmed farm reports from this latter site, however, suggest that a 5–10% mortality of juvenile S. aurata was also caused by an infection of Gyrodactylus, which is suspected to be G. longipes. Additional samples of Gyrodactylus from a gilthead seabream farm located in the north of France have been morphologically identified as G. longipes, extending the geographical distribution of this potentially pathogenic species to three countries and three different coasts. In addition to these samples, some specimens of Gyrodactylus from a Mexican population of rainbow trout were sent for evaluation.
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Herrera, Rodríguez Daniel. "Exploring the Presence and Characteristics of Antibiotic Resistance Genes and Bacteria Present in Water Environments of Uppsala, Sweden." Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416251.
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Antibiotics are one of the greatest discoveries in medicine, and emerged resistances have become a global threat. It is theorized that a big part of the antibiotic resistance genes come from the environment, and wastewater treatment plants and hospitals are considered a great breeding ground for the spread of these. The aim of this project is to analyse the microbiome and resistome of the wastewater of Uppsala and to evaluate the efficiency in the elimination of antibiotic resistance genes and bacteria. Samples from the University Hospital and the influents, sand filter and effluent of the Wastewater Treatment Plant were collected, DNA was extracted and sequenced to be analysed through metagenomics to explore them taxonomically and looking for resistance genes. Bacteria were also isolated, and their resistances were analysed. Taxonomical differences became noticeable in Order, Family, Genus and Species, with an increase of diversity in the Effluent samples. A total of 233 resistance genes were found in all the samples. There was a clear reduction in the number of resistance genes in the Effluent samples. However, there was an important number of genes carried in these and some prevail through all the path. Within all the isolates collected, from a total of 11, three E. coli isolates, one C. freundii and one E. cloacae presented resistances. Our study shows that the effluent of the wastewater treatment plant of Uppsala is potentially causing a negative impact on the environment, flushing out water not completely free of antibiotic resistance genes and resistant bacteria.
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Uchida, Grant K. "Taxonomic treatment of some Hawaiian Psyllidae." Thesis, 1991. http://hdl.handle.net/10125/9772.
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Bamber, Scott. "Trope and taxonomy : an examination of the classification and treatment of illness in traditional Thai medicine." Phd thesis, 1989. http://hdl.handle.net/1885/9441.
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This work is an examination of the classification and treatment of illness in traditional Thai medicine.
The study is based on a nineteenth century compilation of Central Thai court medical texts, as published by the Wat Pho Traditional. Medical Association under the title Phaetsat songkhrQ. Information from this source is supplemented by a synchronic analysis of illness terms in modem Thai, partly derived from interviews conducted with Thais in several regions of Thailand, as well as studies which have been made of other Tai groups.
Drawing upon recent research on cognition and categorisation, the study explores the role played by imaginative processes such as metaphor and metonymy in Thai illness classification and the selection of materia medica. It is argued that through these processes the classification of illness makes an important contribution to the therapeutic process.
An examination of one representative illness category, krasai, which includes a number of illnesses recognised in modem medicine such as kidney disease and hernia, shows that imaginative processes may be involved in classification in several ways. These include numerical symbolism emphasising form rather than content, flexibility in the semantic range of illness categories, and the identification of illness with familiar aspects of the environment, in particular animals.
These processes are also important in determining the treatment of illness. A brief examination of the ingredients found in prescriptions for the treatment of krasai suggests that, apart from any pharmacological value they might possess, their selection is based on various criteria including taste, analogy, and the depiction of illness as a living entity.
Some of the practical implications these findings have for classification theory and the efficacy of traditional medicine are considered.
Books on the topic "Taxonomic treatments"
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Glassman, Sidney F. A taxonomic treatment of the palm subtribe Attaleinae (tribe Cocoeae). Urbana: University of Illinois Press, 1999.
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Juñent, Sergio Roig. The subtribes and genera of the tribe Broscini (Coleoptera, Carabidae): Cladistic analysis, taxonomic treatment, and biogeographical considerations. New York: American Museum of Natural History, 2000.
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Roig-Juñent, Sergio. The subtribes and genera of the tribe Broscini (Coleoptera: Carabidae): Cladistic analysis, taxonomic treatment, and biogeographical considerations. New York: American Museum of Natural History, 2000.
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C, Hickman James, and Jepson Herbarium, eds. Introduction to the Jepson manual: Identification key to California plant families, taxonomic treatment of Saxifragaceae, introductory information. [Berkeley]: Jepson Herbarium and Library, University of California at Berkeley, 1989.
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Christidis, Les, and Walter E. Boles. Systematics and Taxonomy of Australian Birds. CSIRO Publishing, 2008. http://dx.doi.org/10.1071/9780643095601.
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Systematics and Taxonomy of Australian Birds presents an up-to-date classification of Australian birds. Building on the authors’ 1994 book, The Taxonomy and Species of Birds of Australia and its Territories, it incorporates the extensive volume of relevant systematic work since then. The findings of these studies are summarised and evaluated in the explanations for the taxonomic treatments adopted, and with the extensive citations, the book serves as a comprehensive introduction to the recent systematic literature of Australian birds.
All species of birds that have been recorded from the Australian mainland, Tasmania, island territories and surrounding waters are treated and listed. Along with extant native species, all accepted vagrants, recently extinct (since 1800) native species and established introduced species are included.
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Cook, Patricia, Philip Bock, Dennis Gordon, and Haylee Weaver, eds. Australian Bryozoa Volume 2. CSIRO Publishing, 2018. http://dx.doi.org/10.1071/9781486306831.
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Bryozoans are aquatic animals that form colonies of connected individuals. They take a variety of forms: some are bushy and moss-like, some are flat and encrusting and others resemble lace. Bryozoans are mostly marine, with species found in all oceans from sublittoral to abyssal depths, but freshwater species also exist. Some bryozoans are of concern as marine-fouling organisms and invasive species, while others show promise as sources of anticancer, antiviral and antifouling substances.
Written by experts in the field, Australian Bryozoa Volume 2: Taxonomy of Australian Families is the second of two volumes describing Australia’s 1200 known species of bryozoans, the richest diversity of bryozoans of any country in the world. It contains detailed taxonomic data and illustrated family-level treatments, which can be used to identify specimens. It provides an authoritative reference for biology students, academics and others interested in marine biology.
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Linton, Chris, and Susan Howell. Other yeasts. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0013.
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The yeasts described in this chapter are, in general, rare causes of serious human infection. Many are commonly found in the environment or as human commensals. The chapter provides a very brief summary of the following six yeast genera: Malassezia, Rhodotorula, Saccharomyces, Saprochaete, Sporobolomyces, and Trichosporon. Current taxonomy and significant species are also discussed although many fungal taxonomic groups are being re-evaluated in the light of DNA sequencing data, resulting in the renaming of some species and the regrouping of others. Pathogenicity, epidemiology, and clinical aspects are included, and treatment options are discussed. However, as infections caused by these yeasts are uncommon, there is sometimes a lack of supporting data. Culture and identification methods are also summarized, details of which will be presented in other chapters
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Johnson, Elizabeth M. Hyaline moulds. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0017.
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Hyaline moulds are fungi that grow predominantly in a filamentous form with colourless hyphae. This is not a taxonomic grouping and encompasses many thousands of different fungal genera. However, there is a small subset of environmental saprobes or plant pathogenic moulds, currently comprising at least 75 species from 30 different genera, that are opportunistic human pathogens and have been implicated in invasive infections referred to as hyalohyphomycosis. In addition they may cause less invasive cutaneous, subcutaneous, mucous membrane, and corneal infections. This group of organisms includes Fusarium, Sarocladium, Paecilomyces, Purpureocillium, Scedosporium, Rasamsonia, and Scopulariopsis spp., and it is these that form the focus of this chapter. Aspects of taxonomy, cell biology, pathogenesis, epidemiology, incidence, risk factors, presentation, diagnosis, and treatment are discussed with particular reference to those features that are specific to hyaline moulds.
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Bond, Jason E. Phylogenetic Treatment & Taxonomic Revision of the Trapdoor Spider Genus Aptostichus Simon: Aranea, Mygalomorphae, Euctenizidae (Zookeys). Pensoft Pub, 2012.
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Introduction to the Jepson Manual : Indentification Key to California Plant Families, Taxonomic Treatment of Saxifragaceae, Introductory Information. Jepson Herbarium and Library, U of California, 1989.
Find full textBook chapters on the topic "Taxonomic treatments"
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Jauhar, Prem P. "Taxonomic Treatments." In Monographs on Theoretical and Applied Genetics, 9–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-84086-9_2.
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Bernhardt, Nadine. "Taxonomic Treatments of Triticeae and the Wheat Genus Triticum." In Alien Introgression in Wheat, 1–19. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-23494-6_1.
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Argyriou, Thodoris. "The Fossil Record of Ray-Finned Fishes (Actinopterygii) in Greece." In Fossil Vertebrates of Greece Vol. 1, 91–142. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68398-6_4.
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AbstractThe nowadays hyper-diverse clade of Actinopterygii (ray-finned bony fishes) is characterized by a long evolutionary history and an extremely rich global fossil record. This work builds upon 170 years of research on the fossil record of this clade in Greece. The taxonomy and spatiotemporal distribution of the ray-finned fish record of Greece are critically revisited and placed in an updated systematic and stratigraphic framework, while some new fossil data and interpretations are also provided. Greece hosts diverse ray-finned fish assemblages, which range in age from Lower Jurassic to Quaternary. Most known assemblages are of Miocene–Pliocene age and of marine affinities. A minimum of 32 families, followed by at least 34 genera and 22 species, have been recognized in Greece. From originally two named genera and seven species, only two fossil species, established on Greek material, are accepted as valid. Additional taxonomic diversity is anticipated, pending detailed investigations. From a taxonomic perspective, previous knowledge lies on preliminary or authoritative assessments of fossils, with many decades-old treatments needing revision. Little is known about Mesozoic–early Cenozoic occurrences or freshwater assemblages. Given the proven potential of the Greek fossil record, this chapter stresses the need for additional exploration and the establishment of permanent, curated collections of fossil fishes in Greek institutions. Directions for future research are discussed.
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Lichtwardt, Robert W. "Taxonomic Treatment." In The Trichomycetes, 138–273. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4890-3_11.
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Zuloaga, Fernando, and Sandra Aliscioni. "Taxonomic Treatment." In Panicum (Poaceae), 37–274. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-33768-0_9.
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Bremer, Nicholas J. "Taxonomy of Pain." In Deer's Treatment of Pain, 75–77. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12281-2_9.
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Hagen, Ferry, Grit Walther, Jos Houbraken, James Scott, Richard Summerbell, and Teun Boekhout. "Molecular Taxonomy." In Diagnosis and Treatment of Fungal Infections, 31–60. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-35803-6_3.
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Olivere, Lindsey A., and Ranjan Sudan. "A Taxonomy of Errors: Adverse Events and Near Miss Analysis in Bariatric Surgery." In Quality in Obesity Treatment, 283–93. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-25173-4_29.
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Pansarin, Emerson Ricardo, and Ludmila Mickeliunas Pansarin. "Taxonomic treatment of orchid species occurring in the Serra do Japi." In The family Orchidaceae in the Serra do Japi, São Paulo State, Brazil, 31–279. Vienna: Springer Vienna, 2010. http://dx.doi.org/10.1007/978-3-211-99755-0_7.
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Palzer, Andreas, Mathias Ritzmann, and Joachim Spergser. "Mycoplasma hyorhinis and Mycoplasma hyosynoviae in pig herds." In Mycoplasmas in swine, 247–65. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249941.0247.
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Abstract The genetics, taxonomy, epidemiology, prevalence, pathogenesis, clinical signs, diagnosis, treatment, prevention and control of Mycoplasma hyorhinis and M. hyosynoviae in pig herds are described.
Conference papers on the topic "Taxonomic treatments"
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Kanaeva, V. A., and E. I. Olekhnovich. "SEARCH FOR UNIVERSAL METAGENOMIC MARKERS OF THE GUT MICROBIOTA ASSOCIATED WITH THE RESPONSE TO IMMUNOTHERAPY OF VARIOUS TYPES OF CANCER." In OpenBio-2023. ИПЦ НГУ, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-20.
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During the taxonomic analysis of intestinal microbiota samples of patients with various types of cancer undergoing immunotherapy potential biological markers, such as Faecalibacterium prausnitzii associated with a positive outcome of treatment and E. сoli with a negative outcome were identified.
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Al-Abeadi, Rukaya Saad, Ammar A. Suhail, and Anas E. Almousawi. "An overview of Klebsiella pneumoniae: History, taxonomy, epidemiology, pathogenicity, virulence factors and treatment." In 4TH INTERNATIONAL SCIENTIFIC CONFERENCE OF ALKAFEEL UNIVERSITY (ISCKU 2022). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0182174.
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Parodis, I., AE Voskuyl, ME Alarcón-Riquelme, and L. Beretta. "PO.4.92 Taxonomy, treatment, targets and remission in systemic lupus erythematosus: the 3TR-SLE study protocol." In 13th European Lupus Meeting, Stockholm (October 5–8, 2022). Lupus Foundation of America, 2022. http://dx.doi.org/10.1136/lupus-2022-elm2022.118.
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Lythgoe, Mark, Benjamin Mullish, Adam Frampton, Paola Dama, Emily Pickford, Laura Tookman, Paula Cunnea, et al. "627 Oral administration of MRx0518 in treatment-naïve cancer patients is associated with compositional taxonomic and metabolomic changes indicative of anti-tumorigenic efficacy." In SITC 37th Annual Meeting (SITC 2022) Abstracts. BMJ Publishing Group Ltd, 2022. http://dx.doi.org/10.1136/jitc-2022-sitc2022.0627.
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Baier, Christel, Martin Diller, Clemens Dubslaff, Sarah Alice Gaggl, Holger Hermanns, and Nikolai Käfer. "Admissibility in Probabilistic Argumentation." In 18th International Conference on Principles of Knowledge Representation and Reasoning {KR-2021}. California: International Joint Conferences on Artificial Intelligence Organization, 2021. http://dx.doi.org/10.24963/kr.2021/9.
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Abstract argumentation is a prominent reasoning framework. It comes with a variety of semantics, and has lately been enhanced by probabilities to enable a quantitative treatment of argumentation. While admissibility is a fundamental notion in the classical setting, it has been merely reflected so far in the probabilistic setting. In this paper, we address the quantitative treatment of argumentation based on probabilistic notions of admissibility in a way that they form fully conservative extensions of classical notions. In particular, our building blocks are not the beliefs regarding single arguments. Instead we start from the fairly natural idea that whatever argumentation semantics is to be considered, semantics systematically induces constraints on the joint probability distribution on the sets of arguments. In some cases there might be many such distributions, even infinitely many ones, in other cases there may be one or none. Standard semantic notions are shown to induce such sets of constraints, and so do their probabilistic extensions. This allows them to be tackled by SMT solvers, as we demonstrate by a proof-of-concept implementation. We present a taxonomy of semantic notions, also in relation to published work, together with a running example illustrating our achievements.
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Kasrina, Kasrina, Alif Yanuar Zukmadini, Febri Ade Bunga Laily, and Selvia Rahmi. "Medicinal Plants Diversity in Traditional Treatment of Rejang Ethnic Communities in Rejang Lebong Regency as a Resource for Learning Plant Taxonomy." In International Conference on Educational Sciences and Teacher Profession (ICETeP 2020). Paris, France: Atlantis Press, 2021. http://dx.doi.org/10.2991/assehr.k.210227.048.
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Moskvin, A. S. "MORPHOLOGICAL ARTIFACTS ON HISTOLOGIC SPECIMENS OF PARAMPHISTOMIDS (TREMATODA, PARAMPHISTOMIDAE) AND THEIR ROLE IN CORRECT DIAGNOSIS OF SPECIES." In THEORY AND PRACTICE OF PARASITIC DISEASE CONTROL. VNIIP – FSC VIEV, 2024. http://dx.doi.org/10.31016/978-5-6050437-8-2.2024.25.275-279.
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The introduction of a histological method into practice of species diagnostics of trematodes of the suborder Paramphistomata Skrjabin et Schulz, 1937, contributed to regular reports on the discovery of new trematode species in the family Paramphistomidae Fischoeder, 1901. At the same time, several new species were described based on identification of specific histological morphological characteristics which in fact turned out to be artifacts in subsequent detailed analysis. Based on this argument, paramphistomid species described in domestic literature sources, namely, Cotylophoron skrjabini, Cotylophoron vigisi, Ceylonocotyle petrowi, Liorchis hiberniae and Liorchis scotiae are considered as invalid. The cause of morphological artifacts on histological sections of paramphistomids are firstly non–standardized or incorrect primary treatment with fixing chemical agents of parasite isolates detected during necropsy in definitive hosts; secondly, errors in the implementation of general histological technique elements which in the applied approach are critically important and require the development of methodologic modernization adapted to work with biological objects with morphological traits; thirdly, incorrect subjective perception of histological artifacts, their false acceptance as distinctive species characters that have diagnostic value in taxonomy of the family representatives. It is necessary to develop optimized methodological techniques adapted to the applied purpose of teaching methods based on general histological technology elements the implementation of which will help to avoid morphological artifacts on histological sections of paramphistomids.
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Corsiglia, Frederic Anthony, Hani Haidar, and Andrew Duncan Frost. "Risk Informed Work Selection." In Abu Dhabi International Petroleum Exhibition & Conference. SPE, 2021. http://dx.doi.org/10.2118/208015-ms.
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Abstract Asset integrity management is a life cycle concept typically initiated in the conceptual and detailed design phase of projects. Parallel with the development of equipment and system lists, the process of building maintenance job plans starts. Tools, such as criticality assessment, are used to identify the type of engineering deliverable from which the maintenance job plan is built. For a large majority of equipment and systems, original equipment manufacturer (OEM) recommended or fleet inspection, maintenance and testing (IMT) plans are adequate. For a smaller subset, more detailed plans leveraging risk-based inspection (RBI) and reliability-centered maintenance (RCM) concepts are developed building a regime of preventative maintenance focused on data collection in the commissioning and early operation of the facility. For an extremely limited subset of equipment, mostly machinery, but could include pipelines, electrical and product analyzers, the most detailed plans are developed which are highly specific to a particular equipment tag. Criticality assessment is commonly cited as a core process for prioritization of RBI/RCM plan development initially with spare parts inventories and work management later in the life cycle. International standards such as ISO 14224, Petroleum, petrochemical and natural gas industries — Collection and exchange of reliability and maintenance data for equipment, provide a framework for asset hierarchy and taxonomy which will prove to be important during the operating phase of the life cycle where surveillance and corrective maintenance data will be leverage to optimize maintenance job plans. ISO 14224 refers to IEC 60812, Failure modes and effects analysis (FMEA and FMECA), for treatment of Failure Mode Effects and Criticality Assessment (FMECA). To a large extent, ISO 60812 leaves determination of the variables to drive criticality assessment up to the operator saying only that two or more variables should be used. Variables used commonly include consequence of failure, but also maintainability and complexity. Benchmarks for criticality assessment suggest about 10% of equipment merits identification as critical (reference needed). Criticality is important as a foundation to integrity management as work linked to primary function carries an inherited technical characteristic of the equipment and systems. Over time, additional equipment and systems will be added (or removed) from critical equipment lists through continuous improvement processes such as root cause failure analysis (RCFA). With the prioritization of developing maintenance plans through fleet and RBI/RCM processes and their resultant deliverables defined, the detailed plans are identified through collaboration of technical, maintenance and operations staff specialists. Fundamentally, the process involves identification of hazards which can result in impaired primary and secondary functionality, estimation of unmitigated risk, identification of work to mitigate risk, estimation of mitigated risk, calculation of benefit-to-cost and documenting the analysis into the system of record. Consistency in the processes can be assured through application of procedures and references that typically reference a risk matrix. As each hazard is reviewed, there may be multiple failures modes (e.g. hole, crack, rupture) which needs to be considered independently. Consequence assessment is performed for a range of Safety Health Environmental and Security (SHES) scenarios associated with the failure mode. Probability assessment for the scenarios is performed using the available design parameters. The combined consequence and probability form the initial unmitigated risk basis for the scenario. Inspection, maintenance and testing activities are selected by the collaborating specialists with focus of input from technical on probability mitigation, maintenance on cost and operations on benefit. The scenarios is then revisited to document the mitigated risk.
Reports on the topic "Taxonomic treatments"
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Weinberg, Zwi G., Adegbola Adesogan, Itzhak Mizrahi, Shlomo Sela, Kwnag Jeong, and Diwakar Vyas. effect of selected lactic acid bacteria on the microbial composition and on the survival of pathogens in the rumen in context with their probiotic effects on ruminants. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598162.bard.
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This research project was performed in context of the apparent probiotic effect of selected lactic acid bacteria (LAB) silage inoculants on the performance of ruminants (improved feed intake, faster live-weight gain, higher milk yields and improved feed efficiency). The overall objective was to find out how LAB affect ruminant performance. The project included several “chapters” as follows: 1. The effect of LAB silage inoculants on the survival of detrimental bacteria in rumen fluid, in vitro study (Weinberg et al., The Volcani Center). An in vitro model was developed to study the interaction between selected LAB and an E. coli strain tagged with green fluorescence protein (GFP) in buffered RF. Results indicated that both LAB inoculants and E. coli survived in the RF for several days; both LAB inoculants and LAB-treated silages did not affect survival of E. coli in rumen fluid in vitro. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the performance of high-lactating cows (Weinberg et al., The Volcani Center). Treatments included control (no additive), Lacobacillusbuchneri40788 (LB), Lactobacillus plantarumMTD1 40027 (LP) and Pediococcuspentosaceus30168 (PP), each applied at 10⁶ cfu/g FM. The silages were included in the TMR of 32 high milking Holstein cows in a controlled feeding experiment. All baled silages were of good quality. The LB silage had the numerically highest acetic acid and were the most stable upon aerobic exposure. The cows fed the LB silages had the highest daily milk yields, percent milk fat and protein. The microbiome of baled wheat silages and changes during ensiling of wheat and corn (Sela et al., The Volcani Center). Bacterial community of the baled silages was dominated mainly of two genera in total, dominated by Lactobacillus and Clostridium_sensu_stricto_12 with 300 other genera at very low abundance. Fungal community was composed mainly of two genera in total, dominated by Candida and Monascuswith 20 other genera at very low abundance. In addition, changes in the microbiome during ensiling of wheat and corn with and without addition of L. plantarumMTD1 was studied in mini-silos. Overall 236 bacterial genera were identified in the fresh corn but after 3 months Lactobacillus outnumbered all other species by acquiring 95% of relative abundance. The wheat silage samples are still under analysis. The effect of applying LAB inoculants at ensiling on survival of E. coli O157:H7 in alfalfa and corn silages(Adesogan et al., University of Florida). E. coli (10⁵ cfu/g) was applied to fresh alfalfa and corn at ensiling with or without L. plantarumor L. buchneri. The pathogen was added again after about 3 moths at the beginning of an aerobic exposure period. The inoculants resulted in faster decrease in pH as compared with the control (no additives) or E. coli alone and therefore, the pathogen was eliminated faster from these silages. After aerobic exposure the pathogen was not detected in the LAB treated silages, whereas it was still present in the E. coli alone samples. 5. The effect of feeding corn silage treated with or without L. buchnerion shedding of E. coli O157:H7 by dairy cows (Adesogan et al., UFL). BARD Report - Project 4704 Page 2 of 12 Five hundred cows from the dairy herd of the University of Florida were screened for E. coli shedding, out of which 14 low and 13 high shedders were selected. These cows were fed a total mixed ration (TMR) which was inoculated with E. coli O157:H7 for 21 days. The TMR included corn silage treated with or without L. buchneri. The inoculated silages were more stable upon aerobic exposure than the control silages; the silage inoculant had no significant effect on any milk or cow blood parameters. However, the silage inoculant tended to reduce shedding of E. coli regardless of high or low shedders (p = 0.06). 6. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the rumen microbiome (Mizrahi et al., BGU). Rumen fluid was sampled throughout the feeding experiment in which inoculated wheat silages were included in the rations. Microbial DNA was subsequently purified from each sample and the 16S rRNA was sequenced, thus obtaining an overview of the microbiome and its dynamic changes for each experimental treatment. We observed an increase in OTU richness in the group which received the baled silage inoculated with Lactobacillus Plantarum(LP). In contrast the group fed Lactobacillus buchneri(LB) inoculated silage resulted in a significant decrease in richness. Lower OTU richness was recently associated in lactating cows with higher performance (Ben Shabatet al., 2016). No significant clustering could be observed between the different inoculation treatments and the control in non metric multi-dimentional scaling, suggesting that the effect of the treatments is not the result of an overall modulation of the microbiome composition but possibly the result of more discrete interactions. Significant phylum level changes in composition also indicates that no broad changes in taxa identity and composition occurred under any treatment A more discrete modulation could be observed in the fold change of several taxonomic groups (genus level analysis), unique to each treatment, before and after the treatment. Of particular interest is the LB treated group, in which several taxa significantly decreased in abundance. BARD Report - Project 4704 Page 3 of 12
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Parsons, Helen M. Nutrition as Prevention for Improved Cancer Health Outcomes. Agency for Healthcare Research and Quality (AHRQ), May 2023. http://dx.doi.org/10.23970/ahrqepccer260.
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Objective. To understand the evidence base for nutrition interventions delivered prior to or during cancer treatment for preventing and treating negative cancer and cancer treatment–related outcomes among individuals with or at risk for malnutrition. The primary purpose was to inform the National Institutes of Health (NIH) Pathways to Prevention workshop Nutrition as Prevention for Improved Cancer Health Outcomes, held July 26–28, 2022. Data sources. We searched Ovid Medline, Ovid Embase, and Cochrane Central Register of Controlled Trials to identify studies from 2000 through July 2022. We conducted grey literature searches to identify additional resources relevant to the associated costs or value (e.g., cost-effectiveness, cost-benefit) of nutrition interventions. Review methods. The review was guided by a set of Key Questions established by the NIH planning committee for the Nutrition as Prevention for Improved Cancer Health Outcomes workshop. We searched for studies that evaluated a broad range of nutrition interventions (e.g., dietary supplements, nutrition support, nutrition counseling) for preventing and treating negative outcomes of cancer and cancer-related treatment. Eligible studies included randomized controlled trials (RCTs) with enrollment ≥50 participants. We extracted basic study information from all eligible studies, then grouped studies by broad intervention and cancer types. We provide a detailed evidence map for all included studies, but conducted risk of bias and additional qualitative descriptions of outcomes for only those intervention and cancer types with a larger volume of literature. Results. We identified 9,798 unique references, with 206 studies from 219 publications reporting RCTs of nutrition interventions to potentially improve negative outcomes of cancer and cancer-related treatment. Two decades of randomized trial evidence on nutrition interventions for adults prior to and/or during cancer treatment primarily focused on dietary supplements, nutrition support (including oral nutrition supplements), and the route or timing of nutrition interventions for gastrointestinal and head and neck cancers in the inpatient setting. Most studies evaluated changes in body weight/composition, adverse events, length of hospital stay, and quality of life. Few studies were conducted within the U.S. setting. Among intervention and cancer types with a high volume of literature (n=114), which predominantly included studies in dietary supplements and nutrition support in gastrointestinal and head and neck cancers, 11 percent (n=12) were rated as low risk of bias (higher quality), 40 percent (n=46) medium risk of bias, and 49 percent (n=56) high risk of bias (lower quality). Low and medium risk-of-bias studies reported mixed results on the effect of nutrition interventions across cancer and treatment-related outcomes. Although the evidence map shows a large volume of studies evaluating nutrition interventions and outcomes, these studies showed high heterogeneity across study populations, interventions, and outcomes (measure definitions, timing of measurements), even within nutrition intervention categories; as a result, we could not aggregate results. While studies enrolled individuals from multiple cancer types, treatments, and stages, across the lifespan, with varying degrees of muscle wasting, and in those with a range of comorbid conditions, no eligible studies specifically evaluated whether the effects of nutrition interventions on preventing negative outcomes varied across these characteristics. Among studies included in our Key Questions, we found that few (4%, n=8) published cost or value (e.g., cost-effectiveness, cost-benefit) information related to the intervention. In our grey literature search of additional studies examining cost or value of nutrition interventions, we found few studies that conducted cost-effectiveness or cost-benefit analyses; among those that did, we found the studies were conducted in non-U.S. health systems and demonstrated mixed results on the value of nutrition interventions. Conclusions. Although overall RCT evidence focused on a wide range of nutrition interventions, studies were concentrated in use of dietary supplements, nutrition support, and the route or timing of nutrition interventions within gastrointestinal and head and neck cancers in inpatient settings. Among interventions with the highest volume of literature, the majority of studies were rated as high risk of bias. Our findings point to the need for rigorous new research to bolster the evidence base. Specifically, the field needs a more detailed future evaluation of a subset of nutrition interventions contained in this evidence map that focuses on priorities most relevant to specific stakeholders (e.g., oncologists, patients, dietitians, researchers, policymakers). Further, studies should be specifically designed to evaluate the main outcomes of interest for clinical practice. Future research would also benefit from creation of standardized taxonomies for interventions and outcomes as well as more rigorous design and reporting of nutrition interventions. As mentioned, heterogeneity of populations, interventions, comparators, and outcomes precluded aggregation. Currently, the quality and heterogeneity of the studies limit translation of findings into clinical practice or guidelines. In order to inform development of these guidelines, coordinated efforts are required to develop detailed conceptual frameworks for mechanisms of nutrition interventions most relevant to clinical care providers and patients. Such frameworks would help inform priorities for future research as well as guide practice and policy.
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O'Connell, Kelly, David Burdick, Melissa Vaccarino, Colin Lock, Greg Zimmerman, and Yakuta Bhagat. Coral species inventory at War in the Pacific National Historical Park: Final report. National Park Service, 2024. http://dx.doi.org/10.36967/2302040.
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The War in the Pacific National Historical Park (WAPA), a protected area managed by the National Park Service (NPS), was established "to commemorate the bravery and sacrifice of those participating in the campaigns of the Pacific Theater of World War II and to conserve and interpret outstanding natural, scenic, and historic values on the island of Guam." Coral reef systems present in the park represent a vital element of Guam?s cultural, traditional, and economical heritage, and as such, are precious and in need of conservation. To facilitate the management of these resources, NPS determined that a scleractinian (stony coral) species survey was necessary to establish a baseline for existing coral communities and other important factors for conservation. EnviroScience, Inc. performed a survey of stony coral species, coral habitat, and current evidence of stressors at WAPA?s H?gat and Asan Units in 2022. This report summarizes these findings from a management perspective and compares its findings to previous survey data from 1977 and 1999 (Eldridge et al. 1977; Amesbury et al. 1999). WAPA is located on the tropical island of Guam, located on the west-central coast of the island, and encompasses 2,037 acres. Underwater resources are a significant component of the park, as 1,002 acres consists of water acres. The park is comprised of seven units, of which two of these, the H?gat and Asan Beach Units, include all the oceanic water acres for the park. The H?gat Beach Unit (local spelling, formerly known as ?Agat?) is located at the south-west portion of the park and consists of 38 land acres and 557 water acres (NPS 2003). The Asan Beach Unit consists of 109 acres of land and 445 water acres (NPS 2003). A current baseline for existing coral communities and other important factors for conservation necessitates the need for up-to-date data on the location, presence, relative abundance, and present health of corals. Park managers need this updated data to determine where and how to best focus conservation priorities and identify restoration opportunities. Management actions in park reef areas informed by this inventory included identifying locations where there were: high rates of sedimentation; high coral biomass; rare or threatened species, with a priority given to species endemic to Guam and listed as ?threatened? under the U.S. Endangered Species Act (ESA; Acropora globiceps, A. retusa, A. speciosa, and Seriatopora aculeata); coral persistence and decline, disease and/or nuisance species, including the crown-of-thorns starfish (Acanthaster cf. solaris, ?COTS?) and the sponge Terpios hoshinota; and bleached areas. All work carried out was in accordance with the NPS statement of work (SOW) requirements, which involved a quantitative inventory using both new and pre-existing transects. The resulting transects totaled 61 (including the four from the 1999 study), each measuring 50 meters in length and distributed across depths of up to 50 feet. Divers took photo-quadrat samples covering an area of approximately 9 m?, encompassing 50 photo-quadrats of dimensions 0.50 m x 0.36 m (n=50). The collective area surveyed across all 61 transects amounted to ~549 m?. Additionally, a qualitative search was conducted to enhance documentation of coral species that have limited distribution and might not be captured by transects, along with identifying harmful species and stressors. Timed roving diver coral diversity surveys were carried out at a total of 20 sites occurring within the waters of WAPA, including eight sites at the H?gat unit and 12 sites at the Asan unit. The findings from this report reveal significant disparities in benthic cover compositions between H?gat and Asan units. The H?gat unit exhibits high abundances of turf algae and unconsolidated sediment while the Asan beach unit presents a different scenario, with hard coral as the dominant benthic cover, followed closely by crustose coralline algae (CCA). The Asan unit is also more difficult to access from shore or boat relative to H?gat which provides that unit some protection from human influences. The Asan beach unit's prevalence of hard coral, CCA, and colonizable substrate suggests a more favorable environment for reef growth and the potential benefits of maintaining robust coral cover in the area. These distinct differences in benthic communities highlight the contrasting ecological dynamics and habitats of the two study areas. Across both H?gat and Asan beach unit transects, a total of 56 hard coral species were recorded from 27 genera, with 44 species recorded from the H?gat unit and 48 species recorded from the Asan unit. Of the four historical transects surveyed in the Asan unit from 1999, three experienced declines in percent coral cover (17.38-78.72%), while the fourth had an increase (10.98%). During the timed roving diver coral diversity surveys, a total of 245 hard coral species, including 241 scleractinian coral species representing 49 genera and 4 non-scleractinian coral species representing 4 genera were recorded. Uncertainties related to coral identification, unresolved boundaries between morphospecies, differences in taxonomists' perspectives, and the rapidly evolving state of coral taxonomy have significant implications for species determinations during coral diversity surveys. While the recent surveys have provided valuable insights into coral diversity in WAPA waters, ongoing taxonomic research and collaboration among experts will be essential to obtain a more comprehensive and accurate understanding of coral biodiversity in the region. Of the several ESA coral species that were searched for among the H?gat and Asan beach units, Acropora retusa was the only coral species found among quantitative transects (n=2) and A. globiceps was observed during coral diversity surveys. Acropora speciosa, which was dominant in the upper seaward slopes in 1977, is now conspicuously absent from all the surveys conducted in 2022 (Eldredge et al., 1977). The disappearance and reduction of these once-dominant species underscores the urgency of implementing conservation measures to safeguard the delicate balance of Guam's coral reefs and preserve the diversity and ecological integrity of these invaluable marine ecosystems. Other formerly common or locally abundant species were infrequently encountered during the diversity surveys, including Acropora monticulosa, A. sp. ?obtusicaulis?, A. palmerae, Stylophora sp. ?mordax?, Montipora sp. ?pagoensis?, and Millepora dichotoma. Significant bleaching-associated mortality was recorded for these species, most of which are restricted to reef front/margin zones exposed to moderate-to-high levels of wave energy. Sedimentation was present in both H?gat and the Asan units, though it was more commonly encountered in H?gat transects. While significant portions of the reef area within the WAPA H?gat unit are in poor condition due to a variety of stressors, some areas still hosted notable coral communities, which should be a potential focus for park management to prevent further degradation. There is a need for more effective management of point source pollution concerns, particularly when subpar wastewater treatment or runoff from areas with potential pollution or sediment-laden water is flowing from nearby terrestrial environments. Future monitoring efforts should aim to establish a framework that facilitates a deeper understanding of potential point source pollution incidents. This would empower park managers to collaborate with adjacent communities, both within and outside of park boundaries, to mitigate the localized impacts of pollution (McCutcheon and McKenna, 2021). COTS were encountered during transect surveys as well as in coral diversity surveys. including along the upper reef front/reef margin at site Agat-CS-2. The frequency of these observations, particularly in the WAPA H?gat unit and where stress-susceptible corals are already uncommonly encountered, raise concern about the ability of the populations of these coral species to recover following acute disturbance events, and calls in to question the ability of some of these species to persist in WAPA waters, and in Guam?s waters more broadly. More frequent crown-of-thorns control efforts, even if only a handful of sea stars are removed during a single effort, may be required to prevent further loss to vulnerable species. There were several documented incidents of Terpios hoshinota covering large sections of branching coral in the reef flat along transects, but it is still unclear how detrimental this sponge is to the overall reef system. There is a concern that elevated levels of organic matter and nutrients in the water, such as those resulting from sewage discharge or stormwater runoff, could lead to increased Terpios populations (De Voogd et al. 2013). Consequently, it is important to track populations in known areas of sedimentation and poor water quality. The presence of unique species at single survey sites within the study areas underscores the ecological importance of certain locations. Some species are known to occur in other locations in Guam, while a few may be limited to specific sites within WAPA waters. These differences are likely influenced by environmental and biological factors such as poor water quality, severe heat stress events, chronic predation by crown-of-thorns sea stars, disease, and reduced herbivore populations. These factors collectively shape the condition of the benthic community, leading to variations in species distribution and abundance across the study sites. Documenting coral stress and identifying potentially harmful species allows for proactive management strategies to prevent the establishment of nuisance or detrimental species while populations are still manageable. Updated data on the location, presence, relative abundance, and health of corals is essential for park managers to prioritize conservation efforts and identify restoration opportunities effectively. Observations from this report raise concerns about the health and resilience of coral ecosystems in the H?gat unit and emphasize the need for knowledge of local factors that shape benthic community structure. Understanding the drivers responsible for these variations is crucial for effective conservation and management strategies to preserve the ecological balance and overall health of coral reefs in both units. Continued monitoring efforts will be critical in assessing long-term trends and changes in benthic cover and enabling adaptive management approaches to safeguard these valuable marine ecosystems in the face of ongoing environmental challenges.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
Full textAbstract:
Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report