Metadata

Description
Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

Citation
Neto, R R 2006. Organic biogeochemistry of detrital flocculent material (floc) in a subtropical, coastal wetland. Biogeochemistry, 77: 283-304.

Instrumentation
Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector

Description
Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

Citation
Hagerthey, S E 2006. Evaluation of pigment extraction methods and a recommended protocol for periphyton chlorophyll a determination and chemotaxonomic assessment. Journal of Phycology, 42: 1125-1136.

Instrumentation
Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector

Description
Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

Citation
Jaffe, R 2006. Origin and transport of sedimentary organic matter in two subtropical estuaries: a comparative, biomarker-based study. Organic Geochemistry, 32: 507-526.

Instrumentation
Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector