Microbes and Greenhouse Gases

The aim of this study was to characterise the composition of the microbial mats located at the Shanes seep within the coal oil point (COP) seep and investigate whether this contributes to methane oxidisation. The study used ex situ and in situ carbon 13 (¹³C) labelling of methane to monitor the methane uptake by the microbial mat. Also, parallel lipid and DNA analysis was used to look at the abundance and diversity of the mats.

The marine subsurface is a large reservoir for methane, which is important greenhouse gas as it warms the globe 25 times greater than carbon dioxide (Schneising et al., 2009). The micro-organisms, including methanotrophs and methylotrophs, in the water column and seabed utilise some of this methane, limiting the methane released from the sea to the atmosphere. Methanotrophs metabolise methane directly while methylotrophs use methanol and other partially oxidised methane metabolites. The presence of these microbes could be the basis of a food web, creating various niches that encourage a diverse community with important nutrient cycling roles. These microbial mat communities are often dominated by sulfur oxidising bacteria. There have been few studies investigating flow of methane as a carbon source through microbial mats, those that do often looked at dark or low oxygen environments. These studies suggested that the methanotrophy in these environments were mostly anaerobic. However, other studies have shown both anaerobic and aerobic methanotrophs co-occurring in sulfur-oxidising microbial mats, which suggests that shallow oxygen rich environments work in a different manner to the more rigorously researched deep low oxygen communities. To reverse this trend in the literature, this study investigated the microbial mats in COP, which is one of the largest hydrocarbon seeps and a relatively shallow oxygen rich environment (Leifer et al., 2006).

The initial observations showed there was a highly diverse microbial community both within and between mats. This suggests that there could be various metabolic pathways and niches within the community. The diversity of the communities was confirmed with 16S rRNA sequencing. Through assessing the interacting polar lipids (IPL), the study proposed that the mats were mostly bacterial.

To determine if the microbial mats could have an impact on the seeping methane, carbon 13 (¹³C) enriched methane was fed to the microbial mats in a lab setting. The results from this were then extrapolated to represent in situ conditions, and it was estimated that the microbial mats would consume 0.006% of the methane produced, yet it is suggested that the seep stimulates microbial growth as the mats are found within the seep and not outside it. Results from the IPL assessment of ¹³C treated samples suggests that the mats do harbour active methanotrophs as the samples were dominated by Methylcoccaceae, a family of aerobic methanotrophs. This was confirmed by DNA analysis of the samples. Interestingly, this analysis also showed there was diversity and abundance changes between the samples, showing that the microbial mats are complex and poorly understood communities that require further investigation for a deeper understanding of their mechanics.

The study then looked at the methane and CO₂ assimilation in situ by assessing the natural depletion of ¹³C methane and its natural enrichment of CO₂; it found that Methylcoccaceae actively converted the ¹³C methane to biomass within the microbial mats. The biomass was used as a basis for the food web in the mat community and led to a diverse array of organisms comparable to the lab experiment. Additionally, there was evidence of methylophylya activity probably from partially oxidised methane; this activity is caused by organisms indirectly oxidising methane by using methanol. This could increase the efficiency of the consumption of methane by the mat, but further investigation would be needed. Within the mat, further oxidised methane seemed to be used by sulfur-oxidising bacteria, which acquire their carbon from CO₂. They coexist with the methanotrophic/methylotrophic bacteria, and these interactions supplement their CO₂ uptake, which is important as 17% of the gas released by the seep is CO₂.

COP also releases oil and tar along with the gas. Alcanivoraceae, Petrobacter and Oleomonas taxa were found in the top 50 OTUs, suggesting there are various metabolic pathways to degrade ethanol, propanol and butanol, and oxidise aliphatic and aromatic hydrocarbons. This could provide a reasonable explanation to the diversity of the microbial mats, so there are various niches to exploit. There were other functions found within the mats. The abundance of Myxobacteria, characterised by gliding motility, swarming and biofilm development, in several samples suggests that they could drive the initial mat formation. Also, a small eukaryotic phytoplankton population was discovered, which could supply the oxygen for the aerobic activity in the microbial mat. Their growth is enabled by the seeps location within the euphotic zone and could explain the absence of aerobic methanotrophs at deeper seeps.

The study demonstrates the diverse mechanisms for hydrocarbon uptake in seep sediments and characterises a previously uncharacterised seep sediment type. It also shows that there is a huge range of unspecified diversity that, if investigated further, could lead to advances in understanding of microbial degradation of hydrocarbons. This could be used in the event of oil spills. Although the mats acted as a sink for a small fraction of carbon released by the sink, it has shown three main pathways for biomass productivity, which suggests that this is a robust community.

References

Schneising, O., Buchwitz, M., Burrows, J.P., Bovensmann, H., Bergamaschi, P. and Peters, W., 2009. Three years of greenhouse gas column-averaged dry air mole fractions retrieved from satellite–Part 2: Methane. Atmospheric chemistry and physics, 9(2), pp.443-465.

Leifer, I., Luyendyk, B. and Broderick, K., 2006. Tracking an oil slick from multiple natural sources, Coal Oil Point, California. Marine and Petroleum Geology, 23(5), pp.621-630.

Article Reviewed

Paul, B.G., Ding, H., Bagby, S.C., Kellermann, M.Y., Redmond, M.C., Andersen, G.L. and Valentine, D.L., 2017. Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep. Frontiers in Microbiology, 8.