Refers to Flemming, H.-C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-019-0158-9 (2019)

In this month’s issue of Nature Reviews Microbiology, Flemming and Wuertz review the presence of biofilms across the globe1. Before grappling with the numbers, some of which are not very well constrained, one needs to start with the definition of biofilms. One ubiquitous property of microorganisms is their ability to attach to surfaces. These surfaces might be a solid substrate in their environment, the surface of other organisms or the surface of individuals from the same species. When attached cells grow and eventually aggregate in layers, they are termed biofilms2. A common property of biofilms is that cells are embedded in an extracellular matrix of polymeric substances. Biofilms have an important role in many persistent infections, in biotechnological applications3 and in biogeochemical cycles.

Living in biofilms enables complex interactions both between cells and between cells and the matrix of the biofilm, and this can manifest as emergent properties at the community level that are not apparent at the level of individual free-living cells3,4. Acknowledging that biofilms constitute a distinct physiological state of microorganisms, the question arises: how common are biofilms compared with the free-living way of life?

A common statement is that the majority of bacteria and archaea on Earth occur in biofilms3. In contrast to this apparently prevailing state in the wild, laboratory research often relies on free-living microorganisms. The search for a factual basis for the dominance of biofilms leads to a review by Costerton et al. from 1987 (ref.5), which contains a general claim about the ubiquity of biofilms. To date, this has remained speculative, with no supporting data. Flemming and Wuertz revisit this issue and analyse the evidence for the global dominance of biofilms over free-living bacteria and archaea.

The authors integrate data from various quantitative surveys on the abundance of bacteria and archaea within a range of environments. They discuss soils, oceans, the deep subsurface, more minor ecosystems such as commensal bacteria and archaea in abundant animal species, the phyllosphere and also artificial ecosystems such as municipal wastewater. The authors show that five environments dominate in terms of the number of bacteria and archaea. The terrestrial environments are the soil and the deep continental subsurface, which includes the terrestrial subsurface more than 8 metres below ground level. The marine environments include the open ocean, the upper 10–50 cm of the ocean seafloor sediment and the underlying oceanic deep subsurface. Altogether, these environments contain the vast majority of the ≈1030 bacterial and archaeal cells on Earth. Together they weigh approximately 30 gigatonnes of carbon (Gt C = 1015 grams of carbon mass), which corresponds to approximately 6% of the global biomass on Earth. This value for the mass of bacteria and archaea6, presented in Fig. 1, updates a previous estimate of ≈80 Gt C for bacteria and archaea made in a recent global survey7. This update, which decreases the global biomass of bacteria and archaea almost threefold, results from the work of a consortium of researchers who have revised the numbers for the deep subsurface6, showing that they are well below previous estimates and that our view of this habitat is still evolving rapidly.

Fig. 1: The relative contribution of biofilms to the global biomass and population of bacteria and archaea.
figure 1

The analysis by Flemming and Wuertz informs which environments should attract the most focus for further exploration and quantification. Gt C, gigatonnes of carbon.

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Within each environment, Flemming and Wuertz examine the likely fraction of bacterial and archaeal cells living in biofilms. The exact definition of a biofilm can be tricky as surface-attached cells can reside in a continuum of states, from single cells to biofilms. There are data regarding the fraction of cells that are surface-attached relative to planktonic cells in each environment (for example, ref.6). There is also metabolic evidence to suggest that a sizable fraction of those attached cells is active. However, it is not clear how many of those attached cells should be considered as residing in biofilms, as there is no consensus definition of the term. Flemming and Wuertz use a broad definition of biofilms to estimate a somewhat subjective and tentative range of ≈5 × 1029–9 × 1029 bacterial and archaeal cells, or 40−80% of the total number, as being present in biofilms. Of note, this estimate suggests a twofold uncertainty, but the uncertainty may be much larger due to gaps in sampling and quantification as well as to differences in defining biofilms and applying that definition. All of these factors are hard to express in a rigorous confidence interval until more measurements are done. Ultimately, finding the answer to whether biofilms numerically dominate the bacterial and archaeal world remains an open challenge (Fig. 1). The analysis by Flemming and Wuertz informs which environments should attract the most focus for further exploration and quantification. The fact that such a large part of the global biomass and diversity remains so little explored in terms of its mode of life serves to motivate further research that will help answer the question raised by the authors more precisely.

This effort to explore the evidence surrounding a widely accepted narrative in biology joins recent quantitative investigations on fundamental questions such as the ratio between bacterial and human cells in our body8 or the ratio between viruses and bacteria in the ocean9. Such efforts make us revisit what we take to be ‘common knowledge’ and give impetus to further exploration, in this case of the function and distribution of the biofilm communal state, and for a rigorous numerical depiction of the biosphere.