Microbial loop

Talking about food nets the first step that we have to describe is that of the primary producers. Usually, are considered only as “big plants”, while the microorganisms are relegated to the role of decomposers. This is partially true for the terrestrial environment, but wrong in the marine environment, where we find the microbial loop.

Historical hints

Overall, marine bacteria have been considered only as decomposers of organic matter, assuming a trophic network similar to the terrestrial one, where primary production was carried out entirely by algae. In other words, a vision consolidated by the lack of knowledge of the pelagic microbial biome, little known until the years 70/80. To clarify, it was thought that the areas of the open sea, far from the coast, were environments too poor in nutrients, comparable to “marine deserts“.

In 1974, Lawrence Pomeroy hypothesized that marine trophic networks were diametrically different from terrestrial ones, based on microscopic photoautotrophic organisms rather than large plant organisms. But the microbial abundance known for pelagic areas was heavily underestimated, and hardly consistent with that hypothesis.

But in 1977, John Hobbie published a work that was intended to change our view of pelagic environments. He devised a method for visualizing marine microorganisms through nucleoporous filters and epifluorescence microscopy. This revolutionized our view of marine microbiology. In particular, how traditional culturing techniques were inadequate to estimate the diversity of microbial communities that we still can’t cultivate today and led to the concept of microbial loops.

Microbial loop marine bacteria — *Figure 1 – Marine bacteria [Source: Anthony D’Onofrio]*

Difference between marine and terrestrial environment

In the marine environment, the majority of primary production is done by nanoplankton, supported by phytoplankton. If we compare the levels of primary production between the marine and terrestrial environment, the values are quite similar; but looking at biomass and turnover time we have that these values are much lower at sea rather than on land. This with almost five times as much land biomass as is produced with marine biomass.

In fact, while the primary production on the mainland is dominated by the big forests, at sea they are the first superficial meters to have almost all of the production, by phytoplankton and cyanobacteria (very important are the genera Prochlorococcus and Synechococcus).

Why is this structural difference happening? The larger size is a disadvantage in pelagic environments: the scarcity of nutrients, far from the coast, has benefited smaller organisms, strong with a high surface/volume ratio. Thanks to it, they have a greater ability to assimilate nutrients from the environment.

Microbial loop marine bacteria cyanobacteria — *Figure 2 – Filamentous cyanobacteria vs Forest habitat [Source: Doc. RNDr. Josef Reischig; -JvL- from Netherlands]*

The microbial loop: what is it?

The microbial loop is a set of links that connect the pool of dissolved organic substance (DOM) to higher trophic levels through bacterial activity, parallel to the “classic” marine trophic network: phytoplankton -> zooplankton -> secondary and higher-order consumers. Most of the features of the pelagic environment are different from coastal environments: they are oligotrophic zones, poor in nutrients, with well-stratified surface waters that prevent mixing with deep water masses. Moreover, in these environments, the main life forms are the microorganisms and their predators, like protists and bacteriophage viruses.

We can distinguish the organic matter present in the ocean in two main categories: the particulate one (POM) and the already mentioned dissolved (DOM).

Microbial loop: the actors

Cyanobacteria, pelagic bacteria, and Mesopelagic archaea can efficiently exploit dissolved organic matter, assimilating it and sometimes aggregating it to form marine snow (part of the POM). Among pelagic microorganisms we find both autotrophic and photoheterotrophic: the latter can organize the DOM thanks to the bacteriorhodopsin without oxygen production.

The autotrophic and heterotrophic bacterioplankton is grazed by nanoflagellates, predated by ciliates and dinoflagellates; all this allows the re-ingress of the organic substance and the energy that had been released in the environment within the trophic sea networks. Every time there is a transfer of energy from one trophic level to the next there is a certain loss of energy, due to the internal processes of the organisms. This transfer is measured by ecological efficiency. In a pelagic environment, there are a great number of passages to reach the apical consumers, compared to the coastal and upwelling areas, dominated by the diatoms; this brings less energy to the apical consumers, such as the fish, abundant in the upwelling areas.

Marine Bacteria — Figure 3 – Diatoms [Source: *NEON ja*]

In environments where much of the trophic network is directly linked to the microbial loop, pelagic microbial communities tend to remain in a steady-state, although seasonal variations may occur; these conditions are opposed to coastal upwelling areas, where the bloom of single or few species can occur that become dominant in no time.

*Figure 4 – Pelagic trophic network [Source: Clara Ruiz-González]*

An interconnected phenomenon

To sum up, the microbial loop is not an isolated phenomenon, but deeply interconnected with other processes; for example, bacteriophages, through the viral shunt, are one of the forces acting on the microbial loop. The lysis of bacteria by marine viruses allows organic matter to return to the environment in the form of DOM; released substances may be used by other micro-organisms to increase their biomass, thus accelerating the cycles of synthesis and respiration, while a part of the DOM released is by its nature ill-suited to be recycled in the first meters of the water column. This recalcitrant or refractory DOM will then sink, eventually aggregating in POM as marine snow.

The sinking of organic matter, in particular C, due to biological processes, is the focus of the biological carbon pump. It is the set of phenomena that allow the net sequestration of CO₂ from the atmosphere, transferring organic carbon into deep sediments; in the descent, a part of the organic matter will be remineralized, One part will go from POM to DOM and another part will become part of carbonates. However, despite the vertical migrations of organisms and the sinking of organic matter, only a “small” part will reach the bottom, but still such a quantity to consider the sea as a carbon sink.