Tag Archives: Marine Organisms

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.

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.