A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect.

Danny Ionescu,Reza Malekmohammadi,Mina Bizic-Ionescu,Dirk De Beer,Mohammad Reza Morad,Hans-Peter Grossart,Arzhang Khalili

doi:10.1038/srep14706

Abstract

Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). 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 the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods.

Highlights

Particulate organic matter (POM) flow to the deeper parts of water bodies forms a critical link in the global carbon cycle called the “Biological Carbon Pump”[3,4,5]
The flow-through rolling tank devices we present here allow for long term experimentation on any particulate matter at nearly in-situ conditions or with controlled settings
Our experiments clearly demonstrate that in the flow-through rolling tanks the particles were exposed to the same microbial community as in the natural environment

Summary

Introduction

POM flow to the deeper parts of water bodies forms a critical link in the global carbon cycle called the “Biological Carbon Pump”[3,4,5]. This creates the “Bottle Effect”, a phenomenon that has been known for nearly a century[35], in which the natural microbial community is rapidly replaced by opportunistic bacteria[35,36,37,38], alongside an increase in heterotrophic over autotrophic bacteria[39] These changes have profound implications on the microbial activities on the particles, often leading to overestimation of microbial process rates compared to in-situ data[37,40], and even confusing and contradictory conclusions as to whether the oligotrophic ocean is overall heterotrophic[41] or autotrophic[42]. To study the long-term POM dynamics without the bottle effect, we have designed and tested a flow-through rolling tank device This device allows for a continuous flow of water while maintaining the POM aggregates inside in a stable laminar flow-field, thereby allowing us to directly follow the temporal shifts in the diversity and activity of microbial communities on a fine scale under nearly in-situ conditions. The results showed that the microbial community in the closed tank rapidly changed, but that in the flow-through system remained similar to the in situ community for at least 9 days

Methods

Results

Conclusion