you're reading...


One to tango: a bacterium that does the work of two in the nitrogen cycle

van Kessel, M.A.H.J.; Speth, D.R.; Albertsen, M.; Nielsen, P.H.; Op den Camp, H.J.M.; Kartal, B.; Jetten, M.S.M., and Lücker, S. Complete nitrification by a single microorganism. Nature. 24/31 December 2015. doi:10.1038/nature16459.

Complete nitrification by a single bacterium - kind of a big deal, guys!

Complete nitrification by a single bacterium – kind of a big deal, guys!

Nitrogen is an essential element; without it there would be no DNA and no protein—ergo no life. Nitrogen makes up 78 percent of air, where it exists as dinitrogen (or N2), two atoms of nitrogen in a tight bundle inaccessible to plants and animals. Nonetheless, as sure as the grass, the trees, the bees, the cows, you, and I, Nature has its way of “fixing” nitrogen into biologically useful forms like ammonium (NH4+), nitrite (NO2), and nitrate (NO3). The biological nitrogen cycle (terrestrial and marine), which extracts nitrogen from that atmosphere and recycles it back, is driven by a network of prokaryotic microbes (bacteria and archaea) that use nitrogen in its various forms to charge their cellular batteries.

One key process in the nitrogen cycle is nitrification, a two-step process that consists first of the oxidation of ammonium to nitrite, followed by the oxidation of nitrite to nitrate (see feature image). The conventional wisdom on nitrification is that these two steps are performed by distinct bacterial species. However, complete ammonia oxidation (comammox) by a single bacterium is hypothetically possible, and could even be advantageous in certain resource-limiting environments (more energy for your nitrogen when the going gets tough)—so, why not?

“Why not comammox?” is precisely the question asked by a multinational team of scientists lead by Maartje van Kessel and Daan Speth, who, with a pinch of ingenuity and strong dose of patience, bring us the first two examples of comammox bacteria in a recent issue of Nature.

In their quest for comammox, Kessel and Speth et al., first needed a means of enriching for nitrifying bacteria. They did this by collecting the effluent of an aquarium circulating through an oxygen-free compartment (oxygen poisons nitrification) with a filter at the other end fine enough to capture bacteria. To farm nitrifying bacteria, they transferred the filtrate to a minimal growth medium containing low concentrations of the things nitrifying bacteria love most (ammonium, nitrate, nitrite, hold the oxygen). At long last, after a year of sampling in this manner, they obtained a microbial community which removed ammonium from the medium.

Using a technique that allowed them to visualize the species of bacteria growing in their nitrifying microbial community, van Kessel and Speth et al. identified that about half of their culture consisted of Brocadia bacteria, which are known to perform the process of ­anaerobic ammonium oxidation, which is the conversion of one molecule of ammonium and one molecule of nitrite to dinitrogen gas. Interestingly, a group of bacteria identified as Nitrospora that are usually associated with the oxidation of nitrite to nitrate formed a close association with the Brocadia, and made up about 15 percent of the culture. If this doesn’t sound off to you, it should, since both groups of bacteria require nitrite to perform their phylogenetically predicted functions. In other words, these bacteria should be competing with each other, but if they are competing with each other why are they found in a tight association more befitting of a cooperative relationship?

Intrigued by this very question, van Kessel and Speth et al. ground up their culture, and sequenced the the sum total DNA (also called the “meta-genome”) of the enrichment culture. Using computational techniques, they pulled out near complete genomes of the Nitrospora bacteria, and much to their amazement found that these two species contained the genetic potential encoded in a single genetic sentence (a sequential set of genes called an “operon”) to oxidize both ammonium and nitrite—in other words these bacteria looked an awful lot like the comammox bacteria of scientific lore!

To corroborate their genetic predictions, van Kessel and Speth et al. fed specially labeled ammonium to their culture that allowed them to track its fate, and provided experimental evidence for the genetically predicted comammox process. They further confirmed the ammonium-oxidizing activity of the comammox Nitrospora by using specific fluorescent probes to visualize ammonium-oxidizing enzymes in cells tagged as either species of Nitrospora.

To conclude their study, van Kessel and Speth et al. explored the environmental relevance of the newly discovered biological comammox process. Searching available sequence databases with the newly identified ammonium oxidizing genes, Kessel and Speth et al. unearthed previously overlooked bacterial species from environmental hotbeds of ammonium oxidation—wastewater treatment plants, soils, and sediments, hence demonstrating that comammox is more than a mere curiosity.

In revealing an entirely overlooked biological process in the nitrogen cycle central to life on Earth, van Kessel and Speth et al. demonstrate the importance of boldly questioning the status quo to further scientific knowledge. Prior to their finding, researchers dispelled the existence of commamox on the basis that probes for known ammonium oxidizing genes could not identify a bacterium with the full genetic potential to perform complete ammonium oxidation. By taking a step back and questioning textbook understanding, Kessel and Speth et al. made a groundbreaking contribution to an exhaustively studied biogeochemical cycle.


No comments yet.

Post a Comment


  • by oceanbites 2 months ago
    Happy Earth Day! Take some time today to do something for the planet and appreciate the ocean, which covers 71% of the Earth’s surface.  #EarthDay   #OceanAppreciation   #Oceanbites   #CoastalVibes   #CoastalRI 
  • by oceanbites 3 months ago
    Not all outdoor science is fieldwork. Some of the best days in the lab can be setting up experiments, especially when you get to do it outdoors. It’s an exciting mix of problem solving, precision, preparation, and teamwork. Here is
  • by oceanbites 4 months ago
    Being on a research cruise is a unique experience with the open water, 12-hour working shifts, and close quarters, but there are some familiar practices too. Here Diana is filtering seawater to gather chlorophyll for analysis, the same process on
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  on  #oceanbites  we are featuring Hannah Collins  @hannahh_irene  Hannah works with marine suspension feeding bivalves and microplastics, investigating whether ingesting microplastics causes changes to the gut microbial community or gut tissues. She hopes to keep working
  • by oceanbites 5 months ago
    Leveling up - did you know that crabs have a larval phase? These are both porcelain crabs, but the one on the right is the earlier stage. It’s massive spine makes it both difficult to eat and quite conspicuous in
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring Cierra Braga. Cierra works ultraviolet c (UVC) to discover how this light can be used to combat biofouling, or the growth of living things, on the hulls of ships. Here, you
  • by oceanbites 6 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Elena Gadoutsis  @haysailor  These photos feature her “favorite marine research so far: From surveying tropical coral reefs, photographing dolphins and whales, and growing my own algae to expose it to different
  • by oceanbites 6 months ago
    This week for  #WriterWednesday  on Oceanbites we are featuring Eliza Oldach. According to Ellie, “I study coastal communities, and try to understand the policies and decisions and interactions and adaptations that communities use to navigate an ever-changing world. Most of
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Jiwoon Park with a little photographic help from Ryan Tabata at the University of Hawaii. When asked about her research, Jiwoon wrote “Just like we need vitamins and minerals to stay
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring  @riley_henning  According to Riley, ”I am interested in studying small things that make a big impact in the ocean. Right now for my master's research at the University of San Diego,
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Gabby Stedman. Gabby is interested in interested in understanding how many species of small-bodied animals there are in the deep-sea and where they live so we can better protect them from
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Shawn Wang! Shawn is “an oceanographer that studies ocean conditions of the past. I use everything from microfossils to complex computer models to understand how climate has changed in the past
  • by oceanbites 7 months ago
    Today we are highlighting some of our awesome new authors for  #WriterWednesday  Today we have Daniel Speer! He says, “I am driven to investigate the interface of biology, chemistry, and physics, asking questions about how organisms or biological systems respond
  • by oceanbites 8 months ago
    Here at Oceanbites we love long-term datasets. So much happens in the ocean that sometimes it can be hard to tell if a trend is a part of a natural cycle or actually an anomaly, but as we gather more
  • by oceanbites 9 months ago
    Have you ever seen a lobster molt? Because lobsters have exoskeletons, every time they grow they have to climb out of their old shell, leaving them soft and vulnerable for a few days until their new shell hardens. Young, small
  • by oceanbites 9 months ago
    A lot of zooplankton are translucent, making it much easier to hide from predators. This juvenile mantis shrimp was almost impossible to spot floating in the water, but under a dissecting scope it’s features really come into view. See the
  • by oceanbites 10 months ago
    This is a clump of Dead Man’s Fingers, scientific name Codium fragile. It’s native to the Pacific Ocean and is invasive where I found it on the east coast of the US. It’s a bit velvety, and the coolest thing
  • by oceanbites 10 months ago
    You’ve probably heard of jellyfish, but have you heard of salps? These gelatinous sea creatures band together to form long chains, but they can also fall apart and will wash up onshore like tiny gemstones that squish. Have you seen
  • by oceanbites 11 months ago
    Check out what’s happening on a cool summer research cruise! On the  #neslter  summer transect cruise, we deployed a tow sled called the In Situ Icthyoplankton Imaging System. This can take pictures of gelatinous zooplankton (like jellyfish) that would be
  • by oceanbites 11 months ago
    Did you know horseshoe crabs have more than just two eyes? In these juveniles you can see another set in the middle of the shell. Check out our website to learn about some awesome horseshoe crab research.  #oceanbites   #plankton   #horseshoecrabs 
WP2Social Auto Publish Powered By : XYZScripts.com