The research included in this manuscript will allow scientists to better assess the impacts of ocean acidification (OA) on net community production and calcification rates. First, I collaborated with the European Free Ocean Carbon Dioxide Enrichment (eFOCE) project. eFOCE aims to better understand and project the impacts of OA by precisely controlling pH in the field and follow the responses of natural communities. I describe here an incubation-based methodology to study marine benthic community metabolism that takes into account different ecosystem components. I incubate the above ground and below ground aspects of the seagrass community and the below ground separately. This methodology is being developed to investigate the effects of decreasing pH on a seagrass meadow community. Thus one can identify the impact of pH on a whole community and its separate parts. Two partially enclosed chambers were placed in the bay of Villefranche-sur-Mer, in a seagrass community at 12 m depth. In one chamber the pH will be lowered by 0.3 units and maintained at this offset for the long term while the other chamber will serve as a control. For my part of the study, sediment and seagrass incubations were performed separately, in daylight and darkness for 4-24 hours, inside each of the eFOCE chambers. Repeated incubations were conducted in July and September 2013 prior to pH perturbation. Water samples were collected from incubations and changes in dissolved oxygen, dissolved inorganic carbon, and total alkalinity were analyzed to determine net primary production (NPP), community respiration (CR) and, gross primary production (GPP) as well as light and dark net calcification rates. My goal was to assess the status of the meadow and treatment chambers prior to incubation and assess the success of this methodology. The studied seagrass meadow was autotrophic (NCP of ~238 ±123 mmol O2 m-2 d-1, and ~158 ±61 mmol O2 m-2 d-1 in July and September 2013, respectively) and the sediment varied between autotrophic and heterotrophic conditions in July and was clearly heterotrophic in September. The NCPO2:NCPDIC ratio was on average 1.8 for seagrass and 1.9 for sediment. Calcification rates ranged from -107 to -150 mmol CaCO3/m2/day in July. In a separate study, I describe a method to test the validity of the alkalinity anomaly technique often used to determine net calcification rates. Mediterranean mussel, Mytilus galloprovincialis, specimen were incubated for 24 h in a beaker with constant air bubbling. The GCa:GAT ratio based on these measurements was 0.77 ±0.06, uncorrected for alkalinity, and 0.82 ±0.06 when corrected for alkalinity (G*AT). Both ratios are significantly different from the adjusted calcification AT:Ca2+ ratio of 1. The release of dissolved organic carbon could explain the over/underestimation of calcification based on alkalinity. However, most of the produced DOC (Urea) seems to be uncharged and not affect the corrected alkalinity rates. There must be an additional sink of alkalinity that remains unknown. Recently indicated measurements suggested that the ammonium release, which is implemented within the corrected alkalinity rates, was too low. A recalculated G*AT with estimated ammonium release rates gave a GCa:G*AT of 1.09 ±0.08. Within this study the alkalinity anomaly method appears to be not valid for bivalve species; however with the estimated ammonium release taken into account the method seems valid.