Tag Archives: Microorganisms

Activity of Abundant and Rare Bacteria in a Coastal Ocean

It’s been a busy summer, but I’m back to focusing on some recent research.  In fact, there’s been a flurry of recent papers which I plan to highlight here.  I’m exploring fungal and bacterial abundance in forest soils using pyrosequencing techniques with my own research, so I was interested to read this paper on bacterial activity in oceans off the Delaware coast.

In a study from the July 18th early online edition of the journal PNAS, researchers from the University of Delaware and University of Southern California sequenced the bacteria in seawater off the Delaware coast every month over the course of three years.  The research, authored by Barbara Campbell and her colleagues, measured both 16s rDNA and rRNA using next generation pyrosequencing techniques.  By measuring both the presence of DNA (a marker for species presence and overall abundance) and RNA (a marker for relative activity or, more accurately, ribosome activity) in this constantly shifting ecosystem, the authors hoped to explore and understand abundance of both rare and frequently found bacteria in a coastal ocean environment.  I already told you about an article featuring the Rappemonad bacteria, some of which were studied in this paper.

It has been hypothesized in ocean ecosystems that abundant bacteria are found frequently because they have high growth rates and are better at competing against slower growing bacterial.  Conversely, rare bacteria have long been considered to have slower growth rates, just be poor competitors to the more abundant bacteria, or have more streamlined genomes which are better suited to wait in dormancy until the right factor, most likely a specific nutrient, comes into play.

More than 600 OTUs (Operational Taxonomic Units – a term for individuals observed from the environment) were observed and these organisms formed a typical rank abundance curve that we have come to expect from environmental sampling, so there were no surprises in that finding.

What was more surprising, or should I say interesting, was what the authors found by comparing both DNA and RNA from their samples.  After the quality control of their 454 pyrosequencing reads, the authors included more than 500,000 nucleotide samples in their analysis.  More than half of the individual bacteria cycled between abundant and rare during the three years of sampling.  Interestingly, almost half of the bacteria were always considered rare, and close to 12 percent remained rare and inactive, and less than 5 percent were considered to be always abundant throughout the sampling.  The researchers used quantitative RT-PCR to validate specific DNA and RNA concentrations for five separate OTUs to verify the findings from the pyrosequencing portion of the study.

Also quite interesting was that the authors did not observe a pronounced seasonally affected microbial component or an environmental factor that could explain the abundance or scarcity in this ocean environment.  It appears by all accounts that the microbial community observed in this study is constantly changing and may not be regulated by many other factors except the community itself.  See here for a press release from the University of Delaware on this study.

Jacques Monod Conference: Integrative Ecological Genomics

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.

Lessons Learned from Ectomycorrhizal Fungal Genome Sequencing

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)

Newly Identified Branch of Marine Eukaryotes on the Tree of Life

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.

Comparative Genomics Of Eukaryotic Microorganisms Meeting

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.