Tag Archives: Fungi

Biodiversity Monitoring by Plant Proxy is Cheap and Easy: Here’s How and Why

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Post provided by Rasmus Ejrnæs, Ane Kirstine Brunbjerg & Hans Henrik Bruun

Could we use the plants in this swamp forest to predict the diversity of other species?

Local communities and regional biotas are built of hundreds, if not thousands, of species. Most of these species are small-bodied and discreet lifeforms. So it’s no wonder that naturalists have almost always focused their attention on conspicuous species of their particular liking. Why plants then? Well, plants are practical and efficient. They “stand still and wait to be counted”, as the eminent population biologist John Harper put it. No matter the weather, from spring to autumn. There are enough plant species to show contrasts between sites, and yet they can usually be identified to species level in the field.

You Can’t Predict the Diversity of Beetles from Lichens… Can You?

Unfortunately, the overwhelming scientific consensus seems to be that any particular taxonomic group won’t adequately represent the biodiversity of other taxonomic groups. The idea of surrogacy seems to hit the same hard wall as most attempts to provide generally working models for variation in biodiversity at local and regional scales. Biodiversity remains one of the largest scientific research questions without good general answers. Continue reading →

Microbial Methods Virtual Issue

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The BES Microbial Ecology Special Interest Group is running a workshop today (Thursday 2 November) on Novel Tools for Microbial Ecology. To compliment this workshop, Xavier Harrison has edited a Virtual Issue of the best Methods in Ecology and Evolution articles on advances in methods of studying microbial evolution and ecology from the past few years.

Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. The articles in this Virtual Issue cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.

All of the articles in the Microbial Methods Virtual Issue will be freely available for the next two months. You can find out a little more about each one below. Continue reading →

From Star Trek to Species Ranks in Space… and Beyond

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Post provided by Leonardo Saravia

Algae, Space Travel and Jungles

One of my main areas of study is Periphyton developed in microcosms. For those of you who don’t know, Periphyton is a green biofilm that you may notice in some (not very clean) swimming pools and is composed mainly of algae, bacteria, fungi, meiofauna and detritus. I started studying Periphyton because my Masters thesis involved developing a model in freshwater systems and after that I wanted to look into their spatial distribution.

©Hubble Heritage

©Hubble Heritage

I wanted to find an opportunity to connect my study system with two of my passions: space travel (I used to watch Star Trek and also I thoroughly enjoyed Space: The Final Frontier for Ecological Theory by Peter Kareiva) and tropical rainforests (which I developed a fondness for while watching Tarzan). I thought I could use Periphyton as a model system to test ecological theory, with a complexity similar to tropical forest as suggested by Lowe [1].

The study of the spatial structure of Periphyton was not as easy as space travel in Star Trek (for one thing they have a warp drive and I don’t!). I wanted to compare spatial models and data, but the methods that were available weren’t very well-suited to what I wanted to do, so I was not sure of how to begin. In the end, I decided to launch my first microcosms experiment and in the first photos I took of Periphyton’s spatial structure I saw they were like clouds, algae clouds. Continue reading →

Issue 6.8

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Issue 6.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

– LEA: This R package enables users to run ecological association studies from the R command line. It can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets. The package derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results.

– PIPITS: An open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.

Giovanni Strona and Joseph Veech provide this month’s Open Access article. Many studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners, as a method of measuring the structure of ecological networks. In ‘A new measure of ecological network structure based on node overlap and segregation‘ the authors introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species’ tendency against sharing interacting partners).

In addition to this, our August issue features articles on Estimating Diversity, Ecological Communities and Networks, Genetic Distances and Immunology. Continue reading →