http://science.sciencemag.org/content/sci/201/4359/899.2.full.pdf

Phenomenology of perception.

Microbes are the unseen majority in soil and comprise a large portion of lifes genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5‐20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

/pdf/the-unseen-majority-soil-microbes-as-drivers-of-plant-1yjo7xbywu.pdf

The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Climate change 2014 - Synthesis Report

Almost all land plants form symbiotic associations with mycorrhizal fungi. These below-ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, and influence soil structure and ecosystem multifunctionality. Up to 80% of plant N and P is provided by mycorrhizal fungi and many plant species depend on these symbionts for growth and survival. Estimates suggest that there are c. 50 000 fungal species that form mycorrhizal associations with c. 250 000 plant species. The development of high-throughput molecular tools has helped us to better understand the biology, evolution, and biodiversity of mycorrhizal associations. Nuclear genome assemblies and gene annotations of 33 mycorrhizal fungal species are now available providing fascinating opportunities to deepen our understanding of the mycorrhizal lifestyle, the metabolic capabilities of these plant symbionts, the molecular dialogue between symbionts, and evolutionary adaptations across a range of mycorrhizal associations. Large-scale molecular surveys have provided novel insights into the diversity, spatial and temporal dynamics of mycorrhizal fungal communities. At the ecological level, network theory makes it possible to analyze interactions between plant-fungal partners as complex underground multi-species networks. Our analysis suggests that nestedness, modularity and specificity of mycorrhizal networks vary and depend on mycorrhizal type. Mechanistic models explaining partner choice, resource exchange, and coevolution in mycorrhizal associations have been developed and are being tested. This review ends with major frontiers for further research.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.13288

Mycorrhizal ecology and evolution: the past, the present, and the future

Summary
The r package simr allows users to calculate power for generalized linear mixed models from the lme4 package. The power calculations are based on Monte Carlo simulations.
It includes tools for (i) running a power analysis for a given model and design; and (ii) calculating power curves to assess trade-offs between power and sample size.
This paper presents a tutorial using a simple example of count data with mixed effects (with structure representative of environmental monitoring data) to guide the user along a gentle learning curve, adding only a few commands or options at a time.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12504

SIMR: an R package for power analysis of generalized linear mixed models by simulation

Summary
• The contribution of arbuscular mycorrhizas (AM) to plant community structure and diversity is reported here in an annual herbland in southern Australia.
• Mycorrhizal colonization was reduced in field plots by applying the fungicide benomyl as a soil drench. The mycorrhiza-responsiveness of plant species was assessed in intact soil cores containing the indigenous AM fungi and in a pot experiment using an isolate of Glomus mosseae.
• Glasshouse experiments showed that Medicago minima, Vittadinia gracilis and Velleia arguta were highly mycorrhiza-responsive, Salvia verbenaca became colonized but exhibited no growth response to AM, and Carrichtera annua remained uncolonized. There was no change in plant species richness in mycorrhiza-suppressed field plots but diversity increased owing to an increase in evenness. Treatment had no effect on community productivity and therefore there was no relationship between mycorrhizal effects on diversity and productivity.
• Mycorrhizal responsiveness was not a good predictor of species response to suppression of AM in the field. The mycorrhiza-responsive species V. gracilis and V. arguta were not affected by reduced mycorrhizal colonization in fungicide-treated plots, suggesting that competition from the mycorrhiza-responsive dominant M. minima offset the benefits of mycorrhizal association for these species.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1469-8137.2002.00364.x

Arbuscular mycorrhizas influence plant diversity and community structure in a semiarid herbland

Conservation monitoring in Australia has assumed increasing importance in recent years, as societal pressure to actively manage environmental problems has risen. More resources than ever before are being channelled to the task of documenting environmental change. Yet the field remains crippled by a pervasive lack of rigour in analysing, reporting and responding to the results of data collected. Millions of dollars are currently being wasted on monitoring programmes that have no realistic chance of detecting changes in the variables of interest. This is partly because detecting change in ecological systems is a genuinely difficult technical and logistical challenge. However, the failure to plan, fund and execute sophisticated analyses of monitoring data and then to use the results to improve monitoring methods, can also be attributed to the failure of professional ecologists, conservation practitioners and bureaucrats to work effectively together. In this paper, we offer constructive advice about how all parties involved can help to change this situation. We use three case studies of recent monitoring projects from our own experience to illustrate ways in which the disconnect between science and bureaucracy can be bridged and some obstacles to collecting and analysing ecologically meaningful data sets can be overcome. We urge a continuing discussion on this issue and hope to stimulate a change in the culture of conservation monitoring in Australia.

/pdf/making-monitoring-meaningful-2805zg5yih.pdf

Making monitoring meaningful

Summary
This paper reports the successful isolation and preliminary characterisation of a mutant ofLycopersicon esculentumMill. with highly reduced vesicular-arbuscular (VA) mycorrhizal colonization. The mutation is recessive and has been designatedrmc. Colonization byG. mosseaeis characterised by poor development of external mycelium and a few abnormal appressoria. Vesicles were never formed by this fungus in association with the mutant.Gi. margaritaformed large amounts of external mycelium, complex branched structures and occasional auxiliary cells. Small amounts of internal colonization also occurred. Laser scanning confocal microscopy (LSCM) gave a clear picture of the differences in development ofG. intraradicesandGi. margaritain mutant and wild-type roots and confirmed that the fungus is restricted to the root surface of the mutants. The amenability of tomato for molecular genetic characterisation should enable us to map and clone the mutated gene, and thus identify one of the biochemical bases for inability to establish a normal mycorrhizal symbiosis. The mutant represents a key advance in molecular research on VA mycorrhizal symbiosis.

A mutant in Lycopersicon esculentum Mill. with highly reduced VA mycorrhizal colonization: isolation and preliminary characterisation.

Preface. Part 1: A Framework for success . 1 How the book is organised, and why. 1.1 Getting started with writing for international publication. 1.2 Publishing in the international literature. 1.3 Aims of this book. 1.4 How the book is structured. 2 Research article structures. 2.1 Conventional article structure: AIMRaD and its variations. 3 Referees' criteria for evaluating manuscripts. Part 2: When and how to write each article section . 4 Results as 'story': the key driver of an article. 5 Results: turning data into knowledge. 5.1 Figure, table or text?. 5.2 Designing figures. 5.3 Designing tables. 5.4 Figure legends and table titles. 6 Writing about Results. 6.1 Functions of Results sentences. 6.2 Verb tense in Results sections. 7 Methods sections. 7.1 Purpose of the Methods section. 7.2 Organising Methods sections. 7.3 Use of passive and active verbs. 8 Introductions. 8.1 Five 'stages' to a compelling Introduction. 8.2 Stage 1: Locating your project within an existing field of scientific research. 8.3 Using references in Stages 2 and 3. 8.4 Avoiding plagiarism when using others' work. 8.5 Indicating the 'gap' or 'research niche'. 8.6 Stage 4: The statement of purpose or main activity. 8.7 Suggested process for drafting an Introduction. 8.8 Editing for logical flow. 9 Discussion sections. 9.1 Information elements to highlight the key messages. 9.2 Negotiating the strength of claims. 10 Titles. 11 Abstracts. Part 3: Getting your manuscript published . 12 Evaluating journals. 12.1 Considerations when selecting a target journal. 13 Submitting a manuscript. 14 How to respond to editors and referees. 14.1 Rules of thumb for responding to editors and referees. 14.2 How to deal with manuscript rejection. 14.3 How to deal with 'conditional acceptance' or 'revise and resubmit'. 15 A Process for preparing a manuscript. 15.1 Initial preparation steps. 15.2 Editing procedures. 15.3 A pre-review checklist. Part 4: Further developing your publication skills. 16 Skill development strategies for groups and individuals. 16.1 Journal clubs. 16.2 Writing groups. 16.3 Matching feedback strategies to different purposes. 16.4 Training for responding to reviewers. 17 Developing discipline-specific English skills. 17.1 Introduction. 17.2 What kind of English errors matter most?. 17.3 Strategic (and acceptable!) language re-use: Sentence templates. 17.4 More about Noun Phrases. 17.5 Concordancing: a tool for developing your discipline specific English. 17.6 Using the English articles (a/an, the) appropriately in science writing. 17.7 Using 'which' and 'that'. 18 Answer pages. 19 References. Part 5: Provided example articles. 20 Kaiser, B.N., Moreau, S., Castelli, J., Thomson, R., Lambert, A., Bogliolo, S., Puppo, A., & Day, D.A. (2003) The soybean NRAMP homologue, GmDMT1, is a symbiotic divalent metal transporter capable of ferrous iron transport. The Plant Journal, 35, 295-304. 21 Britton-Simmons, K.H. & Abbott, K.C. (2008) Short- and long-term effects of disturbance and propagule pressure on a biological invasion. Journal of Ecology, 96, 68-77.

Patrick O'Connor

Papers

Arbuscular mycorrhizas influence plant diversity and community structure in a semiarid herbland

Making monitoring meaningful

A mutant in Lycopersicon esculentum Mill. with highly reduced VA mycorrhizal colonization: isolation and preliminary characterisation.

Writing Scientific Research Articles: Strategy and Steps

Developing Chinese scientists' skills for publishing in English: evaluating collaborating-colleague workshops based on genre analysis