This week, it’s been hard to miss the new paper, “How many species are there on Earth and in the Ocean?” published by Mora et al. in the August 2011 issue of the journal PLOS Biology. There have been commentaries or news articles printed in the New York Times, The Economist, The Guardian, Damian Carrington’s Guardian Blog, National Geographic, Yahoo News, AlterNet, MSNBC, Reuters, UNEP, NewsDaily and Ed Yong has posted a commentary on his Google+ page. Furthermore, some well respected scientists who study biological diversity have joined the debate too: Jonathan Eisen has devoted two blog posts to the paper (one about the actual paper in PLOS Biology and another on the National Geographic commentary) and there is a commentary from Robert May in PLOS Biology about the study and its significance. Since there is ample information on the study elsewhere, let me communicate a brief summary of the study and some of my feelings about the paper.
It’s quite embarrassing that we have really no clue how much biological diversity is found on this planet. Adding insult to injury is the fact that we have no concept of the current magnitude of the loss of diversity due to human induced mass extinctions. This paper seeks to predict total global biological diversity by documenting current taxonomic numbers and extrapolating consistent patterns to estimate the number of species that have yet to be identified.
The methods of the authors essentially consisted of three parts. First, the authors compiled a list of approximately 1.2 million species pulled from numerous biological databases. Second, they surveyed a little over 500 taxonomists who were asked to identify the validity of current scientific names and comment on the intensity of current taxonomic efforts to describe new species. Third, the authors analyzed this data to find the estimated global numbers of biological taxa for each phylum.
The authors show a predictable pattern in the classification of species (at the phylum, class, order, family, and genus level) at least consistently for animals. By evaluating these patterns using regression, the authors validated this by closely examining 18 taxonomic groups that we think we understand their total biological diversity. By doing this, the authors come up with a total estimate of 7.7 million species of animals (mostly insects), close to 300,000 species of plants, more than 600,000 species of fungi, and a total estimate of roughly 9 million eukaryotes on Earth. The authors estimate that 86% of species on Earth and 91% of species in the oceans still have not been formally described. Previous estimates of species diversity have been wide: anywhere between 3 million to a 100 million species.
This paper is a novel and worthwhile attempt to determine the total amount of species diversity on this planet. Despite this, I think – and the authors have their own reservations – that there are some serious problems with some of their calculations.
One problem is that the study is based mainly on using animals, and vertebrates for that matter – which are the best described of any phylum, as the baseline for measuring the completeness of species diversity. I would argue that plants and fungi, and obviously bacteria, archaea, and “the protists” are clearly not well known enough to extrapolate any serious estimate species numbers especially when considering vertebrate animals as a baseline and whose numbers are largely skewed.
Another problem is in our collective definition of species, as well as taxonomic subjectivity of the categorization of other taxonomic hierarchies, which are based on the on the homology of shared characters and, I would argue, are largely incomparable outside of each phylum. For example, what one taxonomist calls an order in one grouping may not be equivalent to what another taxonomist calls a completely different order in another completely different grouping.
I should point out that the authors don’t ignore these caveats, but they still exist in their study. In any event, this paper is important because it adds to the dialogue concerning species diversity, the need to estimate, inventory and preserve the massive amount of diversity we share on the planet.
Published in the June 2011 issue of the journal Nature Biotechnology was a paper reporting on the genome sequence of the data palm, Phoenix dactylifera. This paper, authored by Al-Dous et al., addressed the genome sequencing and de novo assembly of this agriculturally important monocot tree, along with comparative genomics with other plants.
Dates have been found in the tombs of pharaohs estimated at 8,000 years old. Fields of agriculturally planted trees, estimated to be older than 5,000 years, suggest the date palm is one of the oldest cultivated plants in the world. Dates are the most important agricultural crop in the hot and arid regions surrounding the Arabian Gulf and their global production is close to 7 million tons yearly.
Despite a prolonged emphasis on their agriculture, there are a few problems to deal with if you are a date grower. Typical of tree crops, there is a long generation time from seedling to fruit harvesting. Additionally, only the female date palm provides fruit and it takes at least 5 years after seed germination to tell if you have a male or female plant. To make it even harder for a date grower, there are more than 2000 date varieties, each exhibiting its own color, flavor, size, shape, and ripening schedule, and they are all really hard to keep track of based on conventional techniques.
In an effort to provide genetic resources for date growers and breeders, the authors of this study – who were mainly located in Qutar – sequenced and assembled 380 Mb of the estimated 658 Mb genome of the Khalas cultivar, which is known for high fruit quality. Generated using short reads from the Illumina Genome Analyzer IIx platform, this partial sequence excluded numerous large repeated regions, includes a predicted 28,890 genes, and represented 18 pairs of chromosomes. The authors estimate that this draft genome represents roughly 90% of the total genes and 60% of the total genome.
This genome resource also serves a comparative genomics purpose by being the first member of the widespread monocot order Arecales. To this date, the only Monocots with sequenced genomes – for example: Corn, Rice, and Sorghum – have all been in the grass order, the Poales.
This report is missing some vital information: in addition to an incomplete genome assembly, there is no metabolic, developmental, or gene network pathway reconstruction for the date palm provided in this paper (and unfortunately this paper also includes some glaring typos in the citation section). In place of these expected analyses, the authors conducted a throughout survey of SNPs in this Khalas cultivar, along with eight additional cultivars common in breeding programs for the date palm. Within these nine cultivars, 3,518,029 SNPs were determined, but quite interestingly, a total of 32 SNPs could be used to differentiate the cultivars.
In addition to the throughout SNP analysis, the researchers then did a full parentage analysis of the cultivars used in this study, which includes the famous date varieties such as Deglet Noor, Dayri, and Medjool. Here‘s an article in Nature Middle East on the importance of understanding this parentage and gender analysis.
Although this is a draft genome still being completed and undergoing resequencing, namely the tools provided by the authors, the SNP and parentage analysis, should provide date palm breeders with many resources for improved fruit quality and this genome represents an exciting piece of the monocot evolutionary puzzle.
Registration for the “Genomic Impact of Eukaryotic Transposable Elements” meeting is now open. The meeting will be held February 24th-28th 2012, at the Asilomar Conference Center, in Pacific Grove, California, USA. The conference will consist of invited speakers, general sessions from submitted abstracts, and workshop sessions devoted to computational analysis of transposable elements.
The organizers of the “Second International Conference on the Progress of the “1000 Plant & Animal Reference Genomes Project” have again announced a call for abstracts for the meeting, which will be held from the 10th to 12th of July in Shenzhen, China. I’ve noticed a large increase in the number of meetings in China (see here) and this meeting is also sponsored by the Beijing Genomics Institute (BGI).
As you can gather from the name, the “100 Plant and Animal Reference Genome Project” seeks to provide a total of 1000 plant and animal genomes for the use of researchers (For more information on the “1000 Plant and Animal Reference Genomes Project” see here).
This meeting seeks to increase the number of collaborators, particularly from a global perspective, to this project. To register for this meeting see here, and stay connected to this meeting and the BGI by following them on Twitter (@BGI-Events). You can even enter yourself in a drawing to win a gift (a soft-drink soda!) when you provide proof you have re-tweeted meeting notices from the BGI. The meeting with have two sessions: one on the progress and prospects of the 1000 plant and animal reference genome project and another on new developments in sequencing and bioinformatics technology. There will be five workshops: crop genomics and breeding, aquaculture genomics, vegetable and flower genomics, forest and fruit tree genomics, and rare animal genomics (I’m not really sure what “rare” means in this sense).
Ecological genomics is thriving as a discipline, evidenced by the number of research papers published in this area, and this is due to the large amounts of genomic data now available to researchers. Information from individual genomes, “pan-genomes”, and large scale environmental genome sequencing is giving us a more complete picture of biological diversity.
Some of the top researchers in this newly emerging discipline will be speaking at the Jacques Monod Conference “Integrative Ecological Genomics.” The meeting is held in Roscoff, Brittany, France. Registration is by application (the submission deadline is June 20th 2011) and the number of attendees is capped at 115 people. Information regarding the meeting and registration can be found here and here.
The XV International Congress on Molecular Plant-Microbe Interactions has shaped up to be an amazing meeting. A stellar group of researchers will be presenting at the meeting. Registration is open now.
Directly from the meeting website: “The XV International Congress on Molecular Plant-Microbe Interactions is recognized as the most important international meeting for plant-microbe interactions to discuss research and network with colleagues from around the world. This meeting is the global venue for presenting and discussing new research and developments in molecular plant-microbe interactions. Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research. The meeting features hundreds of abstracts and provides networking and professional development opportunities.”
I’ve already talked about mycorrhizal associations numerous times (here and here), so if you’re not already used to hearing about mycorrhizae, you will if you continue to read this blog. In this recent paper, entitled “Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza“, published online in the journal Nature, the authors Maillet et al address plant and fungal interactions of arbuscular mycorrhizal associations. Using the Glomus intraradices – Medicago truncatula model system, the researchers identify diffusible chemical signals produced by the fungus during initiation of the mycorrhizal association with the plant.
It has been hypothesized that both fungi and bacteria interacting with plant roots do so using similar genetic mechanisms. It has already been shown that rhizobial bacteria – particularly the nitrogen fixing microbes associated with leguminous plants – produce lipochitooligosaccharide (LCO) signals used in the communication with host plants. The authors of this study discovered that the fungus Glomus intraradices, like the nitrogen-fixing bacteria, secretes an array of sulfated and non-sulfated simple LCOs which stimulated the formation of arbuscular mycorrhizae in disparately related plants, such as Medicago (Fabaceae), Daucus carota (Wild Carrot; Apiaceae), and Tagetes patula (French Marigold; Asteraceae). These compounds were found in Glomus intraradices both interacting with plant roots and in free-living resting spores in the soil.
Comparing the genes involved in the transduction of the LCO signals in both rhizobial bacteria associated with legumes and arbuscular mycorrhizal fungi associated with land plants yielded similar gene expression pathways. In order to validate the role of LCOs in mycorrhizae formation, the researchers genetically engineered non-plant interacting bacteria to produce the LCOs from Glomus. These engineered bacteria increased mycorrhizae formation in plants already associated with Glomus. Fungal LCOs were also found to induce root branching, a trait long associated with the formation of mycorrhizae in plants. There is a nice commentary on this research article located here.
Genome sequencing has provided us with an amazing amount of information regarding organismal biology and mycorrhizal fungi are some of the most interesting of the organisms who have had their genomes sequenced. Maybe I am a little partial to these fungi because I study them intimately, but new sequencing technology has made this an exciting time for people like me.
Ectomycorrhizal fungi are a polyphyletic group of organisms which form a symbiotic association with the roots of tree species (the word ‘mycorrhizal’ literally means plant-fungal unions). This association has typically been recognized by the exchange of nutrients and water from the fungus to the plant and the exchange of sugars derived from photosynthesis from the plant to the fungus. Although ectomycorrhizal fungi only form mycorrhizae with 3% of plant species (arbuscular and other mycorrhizal fungi associate with approximately 92% of plants), these associations are with a diverse array of plant lineages, including the Betulaceae, Cistaceae, Dipterocarpaceae, Fabaceae, Fagaceae, Myrtaceae, Pinaceae, and Saleceae. Plants in these families cover almost the entire portion of boreal, temperate, Mediterranean, and sub-tropical woodlands, so their importance is significant. It’s very interesting to note that these associations have independently arisen at least eight times within the angiosperms and between six and eight times in the gymnosperms. Mycorrhizal associations are thought to have originated when plants and fungi climbed onto land together (more on that here).
The sequencing of both fungal and plant genomes over the last few years has led to greater understanding of how these organisms interact during their mutualistic associations. Although genome sequencing has addressed some long established questions, there are many more questions that have arisen from these sequencing efforts. This recent review in Trends in Genetics by Jonathan Plett and Francis Martin of INRA-Nancy, two of my collaborators, addresses the current state of our knowledge of the ectomycorrhizal symbiosis and poses directions for future research in this vital research area.
Currently, only two ectomycorrhizal fungal genomes (Basidiomycete mushroom Laccaria bicolor & Ascomycete truffle Tuber melanosporum) have been sequenced, but other fungi (see the Mycorrhizal Genomes Project) are scheduled to be sequenced by the Martin Lab through JGI. With a genome size of 65 Mb Laccaria bicolor has the largest amount of protein coding regions of any sequenced fungus, and Tuber melanosporum has the largest genome of any sequenced fungus at 125 Mb but has one of the least dense genomes.
The nature of mutualistic symbiotic relationships imply that both organisms benefit from the association and both ectomycorrhizal fungi and their host plants fulfill this criteria. Unlike saprotrophic fungi, ectomycorrhizal fungi are very poorly suited to degrade cellulosic plant material, but they are able to access soil nutrients via a large biological toolbox of secreted proteases and phosphorus transporters. Both Laccaria bicolor and Tuber melanosporum, which have very different genomes, exhibit a very similar suite of symbiosis-induced nutrient cycling enzymes, which suggest that providing nutrients to the host plant is a key defining feature of ectomycorrhizal fungi. Interestingly, Laccaria bicolor and Tuber melanosporum rely on differing mechanisms of interacting with their host and acquiring carbon from the environment. Laccaria bicolor appears to be less dependent on the host and more active at acquiring carbon from the soil substrates and, as a result, may act as a weak saprotroph in the environment. Tuber melansporum is more aggressive in its colonization of plant roots and does not appear to be able to acquire carbon from the soil and therefore is more dependent on the host for its survival.
Information gathered from fungal genomes suggests that a majority of the biochemical and genetic control over the initiation of the mycorrhizal association comes from the fungal partner, which makes sense given that the fungus has more energy to gain from the association. Most mycorrhizal fungi are unable to acquire carbon from the environment so they are completely reliant on hand outs from their host plants. It appears that mutualistic fungi share similar mechanisms with pathogenic fungi and bacteria when interacting with plants, including the use of small secreted proteins which interact directly with plant cells.
With the sheer amount of genomic data being generated it’s an exciting time to be a scientist, especially one who studies mycorrhizal fungi. Over the next few years, especially with sequencing projects scheduled for completion, we will have even more data to shed light on the amazing biological associations of plants and microbes.
(Above Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA)
We’re only just now starting to get a grasp on the sheer amount of global biological diversity, most of which has been very difficult to observe with conventional observational means. Changes in technology and sampling strategies have resulting in the acquisition of information regarding many previously undocumented forms of biological life. Along with microorganisms associated with plant roots – the strict focus on my research interests – phytoplankton represent a large group of organisms that we still know little about. For selfish reasons I was interested in this study because I wanted to see how these authors addressed ways of learning more about a previously unknown lineage of ocean phytoplankton. As evidenced by next generation sequencing efforts, there are many unknown and undescribed fungi in soils and there is a huge amount of commonality of the diversity of microbial life in soils and oceans.
Published in the Proceedings of the National Academy of Sciences, a study entitled “Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life”, by Kim et al, describes a recently identified and previously uncultured marine and freshwater microalgal lineage of Eukaryotic organisms. The researchers title this group of phytoplankton the rappemonads, from the initial paper (authored by Rappé et al 1998) that reported unknown DNA sequences from this lineage. The researchers designed nucleotide primers and fluorescent probes from initial DNA sequences (from the Rappé et al study) and used these molecular diagnostics to observe marine and freshwater samples for their presence or absence of these unknown organisms.
Phylogenetic analysis of environmental nucleotide sequences revealed that rappemonads are related to both haptophyte and cryptophyte algae but constitute a diverse and independent lineage. To resolve the phylogenetic position of the rappemonads the authors designed specific nucleotide primers spanning the 18S-ITS1-5.8S-ITS2-28S rRNA genes and sequenced this gene cluster. The authors used maximum likelihood algorithms to construct a phylogeny, which resolved the rappemonads between the haptophyte and cryptophyte algae. It should be made clear that there is low branch support (at around 50) for some of these clades, so more data is needed for strict resolution of the red plastid algae.
Probes for fluorescent in situ hybridization were developed to observe rappemonads. Rappemonads were described to be relatively large in size – approximately 6 µm in diameter versus the smaller picophytoplankton (2 to 3 µm) – significantly larger than open-ocean phytoplankton. Rappemonads appear to contain two to four plastids and are putatively photosynthetic.
Using quantitative PCR methods, the authors identified high concentrations of rappemonads in late-winter blooms along the surface waters at a site in the Sargasso Sea. Rappemonads were rare or absent in stratified summertime conditions, when concentrations of chlorophyll containing microorganisms are at their highest in deep waters. Rappemonads were frequently found in North Pacific anticyclonic eddy samples, which are characterized by colder more nutrient-rich waters that have been brought to the sea surface. When considering water characteristics (such as depth, salinity, phosphate, nitrate, and nitrite), there were no statistical significance between samples containing rappemonads and those where they were absent. In addition, rappemonads were found in both marine and freshwater conditions, bringing into question when and where one may find these organisms and which would warrant further study.
I’m not sure if I am going to be able to make this meeting, but I thought I would pass on the information to you. The list of speakers is excellent and it’s in a beautiful location. This is a biannual meeting on the comparative genomics of Eukaryotic microorganisms sponsored by the European Molecular Biology Organization (EMBO).
Registration and meeting information is located here.
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