Sulfolane bioremediation

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Title: Factors limiting sulfolane biodegradation in contaminated subarctic aquifer substrate

Argument: Sulfolane is a manmade compound used in petroleum refining. As such, it has no natural metabolic pathway to mineralization known yet. It is also very water soluble so should it spill, it is very likely to create plumes in groundwater. Sulfolane is of interest to the Fairbanks area since we have one such plume originating at the north pole refinery. Several microbiologists are examining sulfolane plumes and growing enrichment cultures from them, hoping to find an organism that has developed a metabolic pathway capable of degrading sulfolane. This is one such paper.


Kasanke CP, Leigh MB (2017) Factors limiting sulfolane biodegradation in contaminated subarctic aquifer substrate. PLoS ONE 12(7): e0181462. pone.0181462


Sulfolane, a water-soluble organosulfur compound, is used industrially worldwide and is associated with one of the largest contaminated groundwater plumes in the state of Alaska. Despite being widely used, little is understood about the degradation of sulfolane in the envi- ronment, especially in cold regions. We conducted aerobic and anaerobic microcosm stud- ies to assess the biological and abiotic sulfolane degradation potential of contaminated subarctic aquifer groundwater and sediment from Interior Alaska. We also investigated the impacts of nutrient limitations and hydrocarbon co-contamination on sulfolane degradation. We found that sulfolane underwent biodegradation aerobically but not anaerobically under nitrate, sulfate, or iron-reducing conditions. No abiotic degradation activity was detectable under either oxic or anoxic conditions. Nutrient addition stimulated sulfolane biodegradation in sediment slurries at high sulfolane concentrations (100 mg L-1), but not at low sulfolane concentrations (500 μg L-1), and nutrient amendments were necessary to stimulate sulfo- lane biodegradation in incubations containing groundwater only. Hydrocarbon co-contami- nation retarded aerobic sulfolane biodegradation rates by ~30%. Our study is the first to investigate the sulfolane biodegradation potential of subarctic aquifer substrate and identi- fies several important factors limiting biodegradation rates. We concluded that oxygen is an important factor limiting natural attenuation of this sulfolane plume, and that nutrient amend- ments are unlikely to accelerate biodegradation within in the plume, although they may bios- timulate degradation in ex situ groundwater treatment applications. Future work should be directed at elucidating the identity of indigenous sulfolane-degrading microorganisms and determining their distribution and potential activity in the environment.

Coupling of anammox and anaerobic methane oxidation in a membrane bioreactor

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Achieving high-level nitrogen removal in mainstream by coupling anammox with denitrifying anaerobic methane oxidation in a membrane biofilm reactor.


Xie, G.J., Liu, T., Cai, C., Hu, S. and Yuan, Z., 2018. Achieving high-level nitrogen removal in mainstream by coupling anammox with denitrifying anaerobic methane oxidation in a membrane biofilm reactor.  Water Research,  131, pp.196-204.


The coupling of carbon and nitrogen cycling in wastewater treatment has implications for shrinking of technologies which would make this strategy (if it is as effective in the real world as the lab) very effective for limited-space applications such as urban, island, and space exploration wastewater treatment.

(Also, I have found a paper that covers both allowed topics: biogeochem and WW treatment)


To achieve energy-neutral wastewater treatment, mainstream anaerobic ammonium oxidation (anammox) has attracted extensive attention in the past decade. However, the relatively high effluent nitrogen concentration (>10 mg N L-1) remains a significant barrier hindering its practical implementation. A novel technology integrating the anammox and denitrifying anaerobic methane oxidation (DAMO) reactions in a membrane biofilm reactor (MBfR) was developed in this study to enhance the mainstream anammox process. With the hydraulic retention time (HRT) progressively decreased from 12 to 4 h, the total nitrogen (TN) removal rate increased stepwise from 0.09 to 0.28 kg N m3 d1 , with an effluent TN concentration below 3.0 mg N L-1 achieved. Mass balance analysis showed that 30-60% of the nitrate produced by the anammox reaction was reduced back to nitrite by DAMO archaea, and the anammox and DAMO bacteria were jointly responsible for nitrite removal with contributions of >90% and <10%, respectively. Additionally, the established MBfR was robust and achieved consistently high effluent quality with >90% TN removal when the influent nitrite to ammonium molar ratio varied in the range of 1.171.55. Fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing indicated that anammox bacteria, DAMO bacteria and DAMO archaea jointly dominated the biofilm, and were likely the key contributors to nitrogen removal. This is the first study that a high nitrogen removal rate (>0.2 kg N m3 d1 ) and satisfactory effluent quality (~3 mg TN L-1) were achieved simultaneously by integrating anammox and DAMO reactions in mainstream wastewater treatment.

ThingLink Cloud microbiology Technical summary

Technical Summary:

Compared to the terrestrial, marine, and limnic environments, the microbial community is relatively unknown in the upper atmosphere (>8 km). Some attempts to measure the lower atmosphere (1 – 7 km) from the tops of mountains have been made, showing that airborne bacteria and fungi from near the ground are lofted by zephyrs and other types of air movement. Studies in the past have also shown that some plant pathogens carry genes for the ice nucleation protein inaZ. If these bacteria were present in the upper atmosphere, they would constitute a major portion of the high-altitude supermicron ice nuclei (particles 0.5 – 3 \( \mu \)m   in size that supercooled water can freeze to). Bacteria are also thought to be meaningful condensation nuclei for cloud formation at lower altitudes.

In this paper, the authors sampled air from the platform of NASA’s aircraft while they were engaged studying the upper atmosphere studying the effects of hurricanes on the upper atmosphere. They sampled ~ 8 m\(^3\) of air with an aerosol spectrometer to estimate the size and abundance of molecules followed by filtration for the sample to perform microscopic counting and qPCR analyses of the small subunit rRNA. They found that there were on average 15,000 cells per cubic meter of air. at high altitude. Most of these were bacteria which do not fall as quickly through the air as do the larger and heavier fungal cell/spores. Analysis of the 16S rRNA gene revealed the vast majority of OTUs were Alpha– and Betaproteobacteria with genera such as Afipia (alpha) and Burkholderiales (beta) making up > 70% of the total reads. Many of the OTUs were in families known to utilize 1-4 carbon molecules in their metabolism, which exist in abundance at that altitude in cloud droplets.

Sampling in the wake of hurricanes Earl and Karl showed that a large portion of the bacterial community resulted from ocean water lofted to altitude and fecal coliforms whenever the hurricane encountered human settlement. In addition, samples taken over land in transit from California, USA to Florida, USA showed that the majority of bacteria were from limnic systems. Together, this suggests that the high altitude bacterial community is primarily supplied by specimens originating in bodies of water that evaporate and are lofted by updrafts and storms.


Paper:  DeLeon-Rodriguez, N., Lathem, T.L., Rodriguez-R, L.M., Barazesh, J.M., Anderson, B.E., Beyersdorf, A.J., Ziemba, L.D., Bergin, M., Nenes, A. and Konstantinidis, K.T., 2013. Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.  Proceedings of the National Academy of Sciences,  110(7), pp.2575-2580.

ThingLink cloud microbiology non-technical summary

Non-technical summary:

Science knows a fair amount about the parts of Earth that can be touched by people. However, not very much is known about microbiology in and above the clouds. A few experiments done earlier suggested that there are microbes in clouds since freshly-fallen snow will “grow’ in a petri dish, clouds have enough of the right chemicals to support microbial life, and the clouds drifting past mountaintops have microbes from lower elevations in them. When cooled to freezing, water needs a small particle to begin crystallizing on, known as an ice nucleus. Some bacteria have special proteins coating them that help water crystallize into ice more easily, and since there were bacteria growing from the snow, it would make sense that the bacteria were serving as ice nuclei. If this is the case, then most of the ice nuclei high in the atmosphere may in fact, be bacteria.

In this experiment, the scientists rode along on a NASA airplane while it was flying ahead of and behind hurricanes Earl and Karl in 2013 doing many other hurricane- and atmosphere-related experiments. The experimenters used a sensor in the airplane that measured how common particles of different sizes were in the air. They then ran the air through a filter that would catch bacteria and took them back to a lab to analyze. In the lab, they examined SSU rRNA, a gene found in all living things to count the bacteria and to identify what the organisms were.

In the air before the hurricanes passed through, most of the bacteria were hardy varieties that could thrive on the chemicals that clouds brought up from the surface. They largely belonged to the Proteobacteria, a group which has a few members known for whacky lifestyles (such as living in frozen ground or inside other cells). After the hurricanes swept through, they found most of the bacteria were from the ocean, except when the hurricanes went over a city, when the bacteria were mostly human fecal bacteria. Based on these findings, the scientists concluded that storms are able to pick up bacteria from near the ground and carry them up into the upper atmosphere where they can help the next generation of clouds condense and fall back down to Earth.


Paper:  DeLeon-Rodriguez, N., Lathem, T.L., Rodriguez-R, L.M., Barazesh, J.M., Anderson, B.E., Beyersdorf, A.J., Ziemba, L.D., Bergin, M., Nenes, A. and Konstantinidis, K.T., 2013. Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.  Proceedings of the National Academy of Sciences,  110(7), pp.2575-2580.


A microbial consortium couples anaerobic methane oxidation to denitrification


Raghoebarsing, A.A., Pol, A., Van de Pas-Schoonen, K.T., Smolders, A.J., Ettwig, K.F., Rijpstra, W.I.C., Schouten, S., Damsté, J.S.S., den Camp, H.J.O., Jetten, M.S. and Strous, M., 2006. A microbial consortium couples anaerobic methane oxidation to denitrification.  Nature,  440(7086), p.918.



Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale1,2. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition3 . In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory4—8. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate9,10. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide11—14 indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.





Methane and nitrous oxide (N2O) are both meaningful greenhouse gasses and are released by thawing permafrost as is observed in the Arctic  in the past five to ten years. This paper outlines a newly-discovered consortium of microorganisms which feeds on methane and is capable of fully denitrifying nitrate to dinitrogen. If this consortium is as prevalent as the authors suggest, then it may be a critical component of remediation in rivers heavily affected by heavy agricultural runoff and melting permafrost deposits.

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Hedges Introduction

Hey everyone,

My name is Ben Hedges. My major is Biology with a concentration in Cell and Molecular Biology and a minor in Mathematics. My fun fact is that I am also a part-time SpaceX Fanboy (TM).

My Haiku:

Large and small in scale,

Tectonic range and microbe.

Both move each other.

The idea was that microorganisms are involved in most if not all of the biogeochemical cycling on Earth including stuff like depositing limestone that later becomes a mountain range. Meanwhile, geographical barriers can form that split a taxon into two groups that become sister species. So the cycle continues, large and small pushing each other around.