Are Traditional Lab Experiments Biasing Our Understanding Of Microbial Processes On Organic Matter Particles?

Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO₂ into aquatic sediments with budget calculations heavily based on the ratio between carbon export and remineralization. Currently microbial dynamics on POM is determined using closed vessels, which are strongly biased towards heterotrophy. We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in closed systems. Photosynthesis and respiration on individual particles in the open system were high for 9 days, double than in a closed system. Using transcriptomics we assessed initial microbial colonization of particles and whether gene expression corroborates rapid changes in carbon-quality. Current understanding is that particle composition, structure and surface properties dictate initial microbial colonization followed by rapid succession events as organic matter lability and nutrient content change during degradation. We used replicate samples of 3–4 particles of identical source and age. The active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. This phenomenon is under further investigation comparing large numbers of individual particles of different sources. Expression of carbon utilization genes didn’t change after 8-9 days of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter, as also suggested by the prolonged high-respiration period. Initial, random particle colonization seems to be followed by multiple organismic interactions shaping community structural and functional dynamics. These results call for reevaluating our mechanistic concepts on microbial activity on POM as well as any experimental data on microbial activity on particles derived from closed systems.