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Understanding the role of microbes in cold seep habitats

Understanding the role of microbes in cold seep habitats

cold seep is an area of the ocean seafloor where hydrogen sulfide, methane and other hydrocarbon-rich fluid seepage occurs. These parts of the ocean floor still remain a large mystery for scientists, in particular for the occurence of hydrothermal vents. In between these vents, microbes live that play a role in the local and global carbon budget. However their exact role remains largerly unknown…

 

Microbes are globally distributed among different environments and catalyze most of the geochemical processes. In cold seep habitats, microbes anaerobically and aerobically oxidize released methane to convert it into carbonate in the sediments or into carbon dioxide above the seafloor respectively (Figure 1).

Fig. 1 Methane consumption by (i) anaerobic oxidation of methane, and (ii) aerobic methane oxidation. (Figure from James et al. 2016).

 

Their role in the global carbon budget is such that anaerobic activity below the seabed may prevent up to 80% of the methane released to reach the atmosphere. However, changes in oceanographic processes can influence the structure and the composition of these microbial communities, that remain poorly understood. These changes may have a cascade effect on the efficiency of methane oxidation. Recently developed methodologies and technologies in molecular biology, such as -omics techniques and fluorescence in situ hybridization, allow scientists to identify active microorganisms and genes associated to their metabolic activities. Additionally, microbes can be isolated through enrichment and cultivation methods. Cultures offer for instance opportunities to test resilience of these microbes to environmental changes, such as temperature and methane concentration variations.

References

James R.H., p. Bousquet, I. Bussmann, M. Haeckel, R. Kipfer, I. Leifer, H. Niemann, I. Ostrovsky, J. Piskozub, G. Rehder, T. Treude, L. Velstade, and J. Greinert. 2016. Effects of climate change on methane emissions from seafloor sediments in the Arctic Ocean: A review. Limnology and Oceanography. 61(S1): S283-S299.

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This blog post was written by Vincent Carrier. He is a PhD student at CAGE (center for arctic gas hydrate, environment and climate) in the University of Tromsø. He is a microbiologist, specialist in DNA analyses of the microbes in methane seep environments. His current research is about to characterize the methanotrophic bacterial communities and the communities responsible for the anaerobic oxidation of methane in different seep environments in the Arctic.

 

Identification of past methane emission altering the foraminiferal tests by secondary overgrowth of calcium carbonate.

Identification of past methane emission altering the foraminiferal tests by secondary overgrowth of calcium carbonate.

Ever heard about foraminifera? These tiny benthic (living at the seafloor) marine organisms are common in oceans across the globe and can be used to accurately give relative dates to sedimentary rocks. But we can also use them to identify past methane emissions from the seabed by studing their test or shell!  

The measurements were done on foraminifera called Cassidulina neoteretis , which is a typical species in Arctic environments and have a hyaline calcareous finely perforated wall that might be altered diagentically. Such diagenesis may occur when the tests experience seafloor methane seepage, of which the sampling was described in a previous blog post. Methane-derived authigenic carbonate (MDAC) crystals precipitate on the exterior and interior test walls, encrusting the test and allowing a detailed analysis of past methane emissions.

upper left: light microscope view of the foraminifera test. Foraminiferal tests having experienced major diagenetic alteration appear “frosty”, with low reflectance and transparency, and yellow to dark brown colour. Upper right: Backscatter Scanning Electron Microscopy image of the exterior test wall. The “frosty” appearance of the tests is caused by methane derived authigenic carbonate (MDAC) precipitation. Lower left: Backscatter-SEM image of a polished wall cross section. Solid MDAC crusts on the interior wall are up to 10 µm thick and appear slightly darker on electron backscatter images due to lower backscatter response of high-Mg calcite compared to foraminiferal calcite.Lower right: Correspondent Energy Dispersive X-ray Spectrometry image. The colour-change from green dominating on pristine foraminiferal calcite test towards a yellow-orange hue reflects higher Mg-content in the MDAC crust (Credit: Andrea Schneider, Centre for Arctic Gas Hydrate, Environment and Climate) .

 

The pictures show what we call the secondary overgrowth of calcium carbonate on these individuals. The benthic foraminifera are well known to calcify their shell in calcium carbonate, but because of the high methane concentration, there is a precipitation of methane-derived authigenic carbonate, which has precipitated on the foraminiferal shell. This is an evidence for past methane emission, which is important to quantify.

Reference:

Hesemann, M., 2017: Cassidulina neoteretis Seidenkrantz, 1995. In: Hesemann, M. 2017 Foraminifera.eu Project Database. Accessed at http://www.foraminifera.eu/single.php?no=1005695&aktion=suche on 2017-9-29


Dr. Pierre-Antoine Dessandier, post-doc researcher at CAGE, center for arctic gaz hydrate, climate and environment, university of Tromso, Norway wrote this blog post. After obtaining his PhD at Bordeaux university (France) in 2015 on micropaleontology, Pierre-Antoine moved to Tromso in Norway to continue his work on benthic foraminiferal ecology and paleo-environments. His main research interests are the use of benthic foraminifera as bio-indicators of climate change and methane emissions in the Arctic seas, using ecology of species and isotopic measurements. He is currently working on active methane seepages in the Barents Sea to reconstruct the chronolgy of the past methane emission and their link with climate change.

 

 

 

Investigation of methane emissions in marine systems

Investigation of methane emissions in marine systems
Ever wondered how we can measure methane emssions from the seafloor ? And ever wanted to steer a mini submarine remotely operating vehicle (ROV)? Well here´s your chance! Have look at this blog post on analyzing methane emissions using ROVs and you´re ready to embark! 

 

The goal is to determine when the gas leak started and how the fluid flow systems work. With our research, we can contribute to a better understanding at what time methane from the seabed has released to the atmosphere and if more emissions have occurred while the climate of the past was changing.

We have been using ROVs to inspect the seafloor and sample carbonate crusts, gas bubbles released from the seafloor and surrounding sediments (Fig. 1).

Fig. 1: the ROV Ægir 6000 (credit:Maja Sojtaric – CAGE).

The last area investigated is composed by two 2 small canyons where a lot of bacterial mats were observed (Fig. 2). These bacterial mats occur where the methane is in high concentration in sediments and represent a target for investigation on methane-influenced systems.

Fig. 2: sampling area in the Norwegian Sea and pictures of the seabed with bacterial mat (credit:Maja Sojtaric – CAGE ).

Two major tools are used in these environments to identify the past methane emissions, the carbonate crusts and push cores.The carbonate crusts precipitated because of the methane release, isotopes measured on these rocks inform about the date of emission and about the source of methane (Fig. 3 and 4).

Fig. 3: Gastropod in CH4-derived carbonate cemented sediment; aragonite botryoids (upper center; X-pol light) (credit: Maja Sojtaric – CAGE).

The push cores are sampled for porewater to trace geochemical processes related to fluid flow processes. Samples are also taken for gas measurements to determine the amount and its sources (Fig. 4). The response of the biological community on methane seepage is analyzed by means of planktonic and benthic foraminifera.

Fig. 4: Push core sampling in bacterial mat (credit: Maja Sojtaric – CAGE).


Dr. Pierre-Antoine Dessandier, post-doc researcher at CAGE, center for arctic gaz hydrate, climate and environment, university of Tromso, Norway wrote this blog post. After obtaining his PhD at Bordeaux university (France) in 2015 on micropaleontology, Pierre-Antoine moved to Tromso in Norway to continue his work on benthic foraminiferal ecology and paleo-environments. His main research interests are the use of benthic foraminifera as bio-indicators of climate change and methane emissions in the Arctic seas, using ecology of species and isotopic measurements. He is currently working on active methane seepages in the Barents Sea to reconstruct the chronolgy of the past methane emission and their link with climate change.

 

 

 

Coffee break biogeosciences–high resolution δ18O record from bivalves

Coffee break biogeosciences–high resolution δ18O record from bivalves

Much like trees, clam shells have growth rings. The chemistry of these rings can be used as a proxy for ocean chemistry. Recently, an international team of scientists used the growth rings found in shells of Arctica islandica to produce an annual absolutely dated marine δ18O record for the last millennium which was published in Nature Communications. The record represents the first fine scale archive longer than ~100 years.   Additionally, it has higher resolution, and less age uncertainty than δ18O records produced from sediment cores.

To read more into what this record means, and the full results of the study see D.J. Reynolds et al, 2016.

Coffee break biogeosciences – New coral reef at Amazon river mouth discovered

Coffee break biogeosciences – New coral reef at Amazon river mouth discovered

At the Amazon river mouth, a huge 9,300 sq km coral reef system has been found below the muddy waters off the mouth of the river Amazon. As corals mostly thrive in clear, sunlit, salt water, and the waters near the mouth of the Amazon are some of the muddiest in the world, the discovery of this almost 2000 km long reef leaves scientists puzzled about the potential extent of coral reefs worldwide.

To find out more about the coral reef at the Amazon river mouth, read  the article by Moura et al. (2016).

 

 

General assembly 2016: our session picks

General assembly 2016: our session picks

Whether you’re an experienced attendee of the EGU GA, or this is your first time there are always things to look out for, it is always worth attending your division’s division meeting, one of the great debates, and keep an eye out for short courses which may be of interest to you. Here are the recommendations from the Biogeosciences Blogging team:

The BG division meeting is Thursday from 12:15-13:15 in Room 1.61.

One short course that could be of interest is Analytical techniques for revealing the nature and chemical properties of natural organic matter on Friday 12:15–13:15 in Room 2.61

Another is Experiments in Geosciences Monday 10:30-12:00 in Room 2.97.

If your work involves samples acquired by drilling the “ICDP-IODP Town Hall meeting” on Tuesday 19:00-start in room G2 could be highly informative.

There are a number of workshops discussing different funding opportunities including the “European research council funding opportunities” on Tuesday with a 19:00 start in room 2.85.

On Wednesday starting at 12:15 is the EGU Early Career Scientists’ Forum in Room L7. One of our contributors (Rachael) is interested in Deep Life, especially in hard rocks.So she is interested in:

  • Monday 8:45-start session entitled “Climate extremes, ecosystems and dynamic landscapes controlling biogeochemical cycles” in room M1
  • Monday 17:30-start session “Fluid circulation in magmatic hydrothermal systems” in room L7

If any of your work involved CO2 storage the session on Thursday starting at 13:30 in Room 2.31 entitled “Field methods and analysis of field data for CO2 geological storage” could be interesting.

If you’re more into climate change related topics such global change ecology, one of our other contributors (Jasper) has some good picks for you:

  • Session about climate extremes and their impact on biogeochemical cycles- monday from 10:30-12:00, room M1
  • Session on the use of plant traits to understand changes in biogeochemical cycles – wednesday from 10:30-12:00, Room M
  • Always wondered how carbon is allocated in plants and ecosystems? If yes, go to the session on plant carbon allocation, 15:30-17:00, room M1
  • How can we use tree rings to understand responses of trees to climate change – thursday from 08:30-10:00, Room 0.3

Finally, it is always interesting to attend at least one session that is completely out of your comfort zone, so you can find out that some scientists are investigating even crazier things than you are currently doing. Our bet for this year’s general assembly: Mars science and exploration! Monday and tuesday from 8:30-10:00, room E1


Post written by Rachael Moore and Jasper Bloemen

Welcome to the multi-faceted world of biogeosciences

Welcome to the multi-faceted world of biogeosciences

“From marine micro-organisms to mountain ecosystems”

Welcome to the official blog of the Biogeosciences (BG) Division of the European Geoscience Union! This blog is run by biogeoscience enthusiasts with very different backgrounds, ranging from plantecophysiology over geology to geomicrobiology. Therefore we think that the variety of posts, will make this blog interesting for all interested in biogeosciences.

We bio‐geoscientists perform research on the processes in and interactions among the Earth’s atmosphere, biosphere, hydrosphere, and geosphere. At first sight, our research might seem very broad and indefinite, but due to the multi‐faceted and interdisciplinary nature of biogeoscientific research, we can provide the scientific basis for understanding the role of ecosystem processes in some of today’smost pressing environmental issues: including, (but not limited to) climate change, deforestation,eutrophication of lakes and rivers, and the effect of sea level rise on coastal and estuarine ecosystems. In addition to all of that, biogeoscientific research informs our understanding of the biogenic signatures found within rocks from early Earth, and areas of our planet which are highly inhospitable.

Benthic foraminifers Mediterranean

Benthic foraminifers recovered from Mediterranean sediments of Neogene age (credit: Aleix Cortina)

Our first blog entry will be on the timing of the closure of the Panama Isthmus which had an important impact on the Great American Biotic Interchange‐ also known as GABIA. Our second blog posts will be on the European Consortium for Ocean Research and Drilling (ECORD) Summer school “Ocean Crust Processes: magma, faults , fluxes, and life” which was recently held in Bremen Germany. Our third post will be on the Amazonian Tall Tower Observatory (Atto) in the Brazilian rain forest which was inaugurated last month and will be used to measure greenhouse gases, aerosol particles, cloud properties, boundary‐layer processes, far away from human influences. In a later stage we foresee blog contributions from scientists with a wide range of biogeoscientific backgrounds. If you would like to write a blog entry about your research, please get in touch with the editor, especially if you are an early career scientist! We welcome all contributions that fit broadly within the topic of Biogeosciences.