Abundance of isoGDGTs and archaeal gene copies in suspended particulate matter and settling particles from Lake Chala, East Africa

For the analysis of suspended particulate matter, 5-10 L of lake water was collected at 13 discrete depths between the lake surface and 90 m depth, monthly between September 2013 and January 2015 (n = 221). The samples were filtered on pre-combusted glass fiber GF/F filters (142 mm diameter, Whatman), stored frozen and freeze-dried prior to analysis. Core lipid (CL) isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) in the SPM from all depths for the months of November 2013 and August 2014, and from 0, 10, 25, 35, 50, 60, 70 and 80 m depth for the 15 other months (total n = 141) were analyzed. In addition, we analyzed intact (IPL) isoGDGTs in SPM from 20, 30, 45 and 90 m depth collected in December 2013, April 2014 and September 2014. The freeze-dried SPM filters were cut in small pieces and extracted using a modified Bligh-Dyer method (Bligh and Dyer (1959; doi:10.1139/o59-099). The CL GDGTs present in the polar fractions were analyzed by ultrahigh-performance liquid chromatography (UHPLC) following the method of Hopmans et al. (2016; doi:10.1016/j.orggeochem.2015.12.006), using an Agilent 1260 Infinity UHPLC system coupled to an Agilent 6130 single quadrupole mass detector. IPL GDGTs in SPM samples were extracted from the freeze-dried filters using a modified Bligh Dyer extraction and analyzed using Ultra High Pressure Liquid Chromatography-High Resolution tandem Mass Spectrometry (UHPLC-HRMS2) according to the method of Wörmer et al. (2013; doi:10.1016/j.orggeochem.2013.03.004) with modifications as described by Bale et al. (2019; doi:10.3389/fmicb.2019.00589). DNA was extracted from a small section (1/32) of the all collected SPM filters, using the PowerSoil DNA extraction kit (Mo Bio Laboratories, Carlsbad, CA, USA). The 16S rRNA gene amplicon sequencing and analysis was performed with the general 16S rRNA archaeal and bacteria primer pair 515F and 806RB, targeting the V4 region as described by Besseling et al. (2018; doi:10.5194/bg-15-4047-2018). PCR products were gel-purified using the QIAquick Gel-Purification kit (Qiagen), pooled and diluted. In November 2006 a UWITEC® double-funneled sediment trap of 86 mm diameter was installed at 35 m water depth in a mid-lake position, and emptied and redeployed at approximately monthly intervals during the following 8 years. Collected material was allowed to settle for two days, and stored frozen after decantation of excess water. Prior to analysis, the samples were thawed, filtered over pre-weighed and pre-combusted (400 ºC, 5h) glass fiber GF/F filters (110 mm diameter, Whatman), frozen and freeze-dried. The settling particle data combines new analyses of GDGTs in settling particles representing the period September 2010 to January 2015, with published data for the period November 2006 to August 2010 (Sinninghe Damsté et al., 2009 (doi:10.1016/j.gca.2009.04.022); Buckles et al., 2014 (doi:10.1016/j.gca.2014.04.042), 2016 (doi:10.5194/cp-12-1243-2016)), also sampled at near-monthly intervals, to cover a total of > 8 years (n = 98 total samples)