Microbial activity in marine sediment constrained via lipid-based stable isotope probing

Abstract

Microbial-driven organic matter mineralization in marine sediment plays a vital role in the global carbon cycle. However, microbial activities and metabolisms in this environment are poorly constrained. This thesis aimed to quantitatively assess microbial activity by using a lipid-based stable isotope probing (SIP) method. Compared with 13C- or 15N-labelled organic substrates, dual labelling with D2O and 13C-inorganic carbon (IC) substrates serves to estimate in situ microbial activity with minimal distortion of in situ nutrient conditions. This approach provides an estimate of total microbial activity and can distinguish microbial metabolisms based on the ratio of incorporation of 13C-IC vs D2O (R13C/D) into microbial lipids (cf. Wegener et al., 2012). However, the current working hypothesis is based solely on the cultivation of the Deltaproteobacterium Desulfosarcina variabilis and thus poorly constrained. Therefore, additional empirical evidence is required for broad scale application of this proxy, e.g., to archaea. To extend the application of this dual SIP method, the methanogen archaeon Methanosarcina barkeri was incubated with D2O and 13C-IC under different conditions (H2/CO2, acetate and methanol; Chapter II). Incorporation of IC and water-derived H were dependent on the carbon substrates used for growth. The relatively low water H contribution ( 40%) to lipids yielded an increased R13C/D ratio that exceeded the assumed upper limit of 1 (cf. Wegener et al., 2012). This finding invokes more investigation of water H contribution to microbial lipids in order to quantitatively estimate microbial activity in environmental settings. By using the dual SIP method, this thesis further investigated the microbial activities and metabolisms in surface costal sediments under in situ sulfate-reducing conditions including an intertidal sediment from Janssand (Wadden Sea, Germany; Chapter III) and estuarine sediment from the Rhone River prodelta (Gulf of Lions, France; Chapter IV). Average turnover times of bacteria and archaea populations were 7.4 and 110 years, respectively. Compared with archaea, IC was significantly incorporated into bacterial fatty acids in surface sediments, with the assimilation rates ranging from 0.15 to 1.3 A g gdw-1 yr-1. Furthermore, R13C/D of bacterial fatty acids ranged from 0.07 to 0.23, indicating that heterotrophic bacteria were dominant and measured inorganic carbon fixation rates likely resulted from their anapleurotic reactions. To further explore the potential for IC assimilation among Archaea, a surface estuarine sediment (upper 10 cm) from Hangzhou Bay (East China Sea, China; Chapter V) was incubated anaerobically with different organic substrates (i.e., casein, oleic acids, cellulose, phenol and lignin) and 13C-IC. Only the addition of lignin stimulated the growth of Bathyarchaeota (formerly referred as Miscellaneous Crenarchaeotal Group, MCG) and resulted in 13C-labelling of their putative lipids. Together, these results suggest that Bathyarchaeota can use lignin as an energy source and IC as a carbon source. The demonstration of Bathyarchaeota metabolism of lignin sheds new light into microbial carbon cycling and important energy substrates for microbial populations in marine sediments. This thesis quantitatively assessed microbial activity and compared the difference between bacterial and archaeal activity in surface marine sediment via lipid-based SIP method. The findings suggest that dark inorganic carbon fixation may be an important consequence of heterotrophic microbial activity in marine sediment and should be considered as important role for constraining sedimentary C fluxes in the biogeochemical carbon cycle.