Microbial Ecology
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Rescooped by Jorge Sáenz Mata from Plants and Microbes
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Frontiers: Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens (2014)

Frontiers: Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens (2014) | Microbial Ecology | Scoop.it

The plant tumor disease known as crown gall was not called by that name until more recent times. Galls on plants were described by Malpighi (1679) who believed that these extraordinary growth are spontaneously produced. Agrobacterium was first isolated from tumors in 1897 by Fridiano Cavara in Napoli, Italy. After this bacterium was recognized to be the cause of crown gall disease, questions were raised on the mechanism by which it caused tumors on a variety of plants. Numerous very detailed studies led to the identification of Agrobacterium tumefaciens as the causal bacterium that cleverly transferred a genetic principle to plant host cells and integrated it into their chromosomes. Such studies have led to a variety of sophisticated mechanisms used by this organism to aid in its survival against competing microorganisms. Knowledge gained from these fundamental discoveries has opened many avenues for researchers to examine their primary organisms of study for similar mechanisms of pathogenesis in both plants and animals. These discoveries also advanced the genetic engineering of domesticated plants for improved food and fiber.


Via Kamoun Lab @ TSL
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Rescooped by Jorge Sáenz Mata from Plant-Microbe Symbiosis
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Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

Assessing Bacterial Diversity in the Rhizosphere of  Thymus zygis  Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches | Microbial Ecology | Scoop.it
Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

Via Jean-Michel Ané
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Rescooped by Jorge Sáenz Mata from Microbe-Microbe Interactions and miscellaneous
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Resources for academic writing and publishing

 

I led a workshop on academic writing and publishing last week, and this is a list of resources I gave to the participants. It's not an exhaustive list, so if you have any favorites let me know and I'll add them!

 

Links and resources

 

General writing resources

 

Strunk, W. Jr. (1999).The Elements of Style. http://www.bartleby.com/141/

 

 

 

Guidelines and lessons for good scientific writing

 

Cargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1444356216.html

 

Doumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. http://www.nature.com/wls/ebooks/english-communication-for-scientists-14053993/contents (Free ebook - very useful)

 

Duke University Graduate School. Scientific Writing Resource.  https://cgi.duke.edu/web/sciwriting/index.php Short, online course for graduate students with examples and worksheets

 

Editorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139. http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html

 

European Association of Science Editors. EASE Toolkit for Authors. http://www.ease.org.uk/publications/ease-toolkit-authors

 

Nature Scitable Effective Writing. http://www.nature.com/scitable/topicpage/effective-writing-13815989

 

Nature Scitable Scientific Papers. http://www.nature.com/scitable/topicpage/scientific-papers-13815490

 

Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).

 

Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007. http://www.elsevier.pt/en/linkresolver/320/how-to-write-scientific-paper-and-win/90020266

 

Plaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009394/pdf/pro0019-2261.pdf

 

Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer. http://www.springer.com/medicine/book/978-3-642-39445-4https://moodle.swarthmore.edu/pluginfile.php/179173/mod_resource/content/1/Good%20versus%20poor%20scientific%20writing%20from%20Silvia%20Rogers.pdf

 

Writing Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines. http://writing.wisc.edu/Handbook/ReverseOutlines.html

 

 

 

Guidance from journals

 

J Exp Bot: http://www.oxfordjournals.org/our_journals/exbotj/for_authors/

 

Nature: http://www.nature.com/authors/author_resources/how_write.html

 

Plant Cell: http://www.plantcell.org/site/misc/ifora.xhtml

 

 

 

Figures preparation and ethical issues

 

Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4. http://www.plantphysiol.org/content/163/1/3.short

 

Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667

 

Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15. http://jcb.rupress.org/content/166/1/11.short

 

 

 

Peer Review Guidelines and Policies, Post-publication peer review

 

Bastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772

 

F1000Research: http://blog.f1000research.com/2014/07/08/what-is-post-publication-peer-review/

 

F1000: http://journal.frontiersin.org/Journal/10.3389/fncom.2012.00063/full

 

Mole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144. http://hwmaint.jcs.biologists.org/cgi/reprint/120/7/1143

 

Nature: http://www.nature.com/authors/policies/peer_review.html

 

Office of Research Integrity. (US Dept of Health and Human Services) The Lab. http://ori.hhs.gov/THELAB

 

Office of Research Integrity. Research Clinic Case Book. http://ori.hhs.gov/rcr-casebook-stories-about-researchers-worth-discussing

 

Science: http://www.sciencemag.org/site/feature/contribinfo/review.xhtml

 

PLOS ONE:www.plosone.org/static/reviewerGuidelines

 

Provenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99. http://tech.snmjournals.org/content/34/2/92.full.pdf+html

 

Times Higher Education: http://www.timeshighereducation.co.uk/news/can-post-publication-peer-review-endure/2016895.article

 

 

 

Readability

 

RavenBlog (2010). Ultimate list of online content readability tests. http://blog.raventools.com/ultimate-list-of-online-content-readability-tests/

 

 

 

Communicating more broadly

 

Kuehne, L.M., et al. (2014). Practical science communication strategies for graduate students. Conservation Biology. 28: 1225–1235. .DOI: 10.1111/cobi.12305

 

Osterrieder, A. (2013). The value and use of social media as communication tool in the plant sciences. Plant Methods. 9: 26. http://www.plantmethods.com/content/9/1/26

 

 

 


Via Mary Williams, Nina Dombrowski
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Bibhya Sharma's curator insight, February 3, 2015 8:58 PM

Very helpful for teachers and researchers. 

Andres Zurita's curator insight, February 4, 2015 12:53 PM
Outstanding source of fine material! Thanks Mary!
Rescooped by Jorge Sáenz Mata from The Plant Microbiome
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mBio: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

mBio: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats | Microbial Ecology | Scoop.it

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.


Via Stéphane Hacquard
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Structure, variation, and assembly of the root-associated microbiomes of rice

Structure, variation, and assembly of the root-associated microbiomes of rice | Microbial Ecology | Scoop.it
Using rice as a model, we show that there exist three different root niches hosting different microbial communities of eubacteria and methanogenic archaea. These microbial communities are affected by geographical location, soil source, host genotype, and cultivation practice.

Via Mary Williams
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Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes | Microbial Ecology | Scoop.it

Given the recently appreciated complexity of symbioses among hosts and their microbes, significant rethinking in biology is occurring today. Scientists and philosophers are asking questions at new biological levels of hierarchical organization - What is a holobiont and hologenome? When should this vocabulary and associated concepts apply? Are these points of view a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Legitimate questions, advancements and revisions are warranted at this nascent stage of the field. However, a productive and meaningful discourse can only commence when skeptics and proponents alike use the same definitions and constructs. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not necessarily the primary unit of selection is not synonymous with arguing that it is not a unit of selection in general. Here, we succinctly deconstruct and clarify these recent misconceptions. Holobionts (hosts and their microbes) and hologenomes (all genomes of the holobiont) are multipartite entities that result from ecological, evolutionary and genetic processes. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome. We invite the community to consider these new perspectives in biology.


Via Stéphane Hacquard
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Ryohei Thomas Nakano's curator insight, February 3, 2016 3:46 AM

[ For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not necessarily the primary unit of selection is not synonymous with arguing that it is not a unit of selection in general. ]

 

Absolutely.

Rescooped by Jorge Sáenz Mata from Microbe-Microbe Interactions and miscellaneous
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PNAS: Root surface as a frontier for plant microbiome research

Plants associate—analogous to animals or us humans—with a multitude of microorganisms, which collectively function as a microbiome. A major discovery of the last decade is that numerous organisms of a microbiome (aka microbiota) are not unpretentious background actors. Instead, some microbiota members influence host processes including behavior, appetite, and health in animals (1) and contribute to nutrition and health of plants (2–4). Recently, the compositions of the plant root-associated microbiota from numerous plant species, including major crops, were revealed using high-throughput DNA sequencing. Factors such as soil type or host genotype influence the root-associated microbiota. However, the processes that determine the acquisition of the root microbiota, its resistance to stress, and its ecological function remain poorly understood. Edwards et al. (5) present the third publication in a recent series of PNAS articles about the bacterial microbiota associated with plant roots of maize (6), related Brassicaceae (7), and now Oryza sativa (rice). It comprises a comprehensive characterization of three microbial habitats that are in the proximity of, on, and inside plant roots, which are named rhizosphere, rhizoplane, and root endosphere (Fig. 1).


Via Stéphane Hacquard, Nina Dombrowski
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The Plant Microbiome at Work

The Plant Microbiome at Work | Microbial Ecology | Scoop.it

Plants host distinct microbial communities on and inside their tissues designated the plant microbiota. Microbial community profiling enabled the description of the phylogenetic structure of the plant microbiota to an unprecedented depth, whereas functional insights are largely derived from experiments using individual microorganisms. The binary interplay between isolated members of the plant microbiota and host plants ranges from mutualistic to commensalistic and pathogenic relationships. However, how entire microbial communities capable of executing both growth-promoting and growth-compromising activities interfere with plant fitness remains largely unknown. Ultimately, unravelling the net result of microbial activities encoded in the extended plant genome—the plant microbiome—will be key to understanding and exploiting the full yield potential of a crop plant. In this perspective, we summarize first achievements of plant-microbiome research, we discuss future research directions, and we provide ideas for the translation of basic science to application to capitalize on the plant microbiome at work.


Via Nina Dombrowski
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Rescooped by Jorge Sáenz Mata from Plant Biology Teaching Resources (Higher Education)
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Super schedule of speakers, PlantBiology2015 (26-30 July 2015)

Super schedule of speakers, PlantBiology2015 (26-30 July 2015) | Microbial Ecology | Scoop.it

See the full schedule here - minisymposium speakers TBA


Via Mary Williams
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Diversity of culturable thermo-resistant aquatic bacteria along an environmental gradient in Cuatro Cienegas, Coahuila, Mexico

Diversity of culturable thermo-resistant aquatic bacteria along an environmental gradient in Cuatro Cienegas, Coahuila, Mexico | Microbial Ecology | Scoop.it
Diversity of culturable thermo-resistant aquatic bacteria along an environmental gradient in Cuatro Cienegas, Coahuila, Mexico - Science Alerts Social Network
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