Does the Environment “Filter” or “Select” Species? Bridging the Ecologies of Microbes and Macro-Organisms for a Common Niche Assembly Theory

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Review of the paper

The Environment “Filters” or “Selects” Species? Bridging the Ecologies of Microbes and Macro-organisms for a common niche assembly theory

by Rutger De Wit

 

The paper is a useful and interesting contribution. It discusses theoretical approaches how to understand and interpret biodiversity development processes of microbiota and macrobiota. For them, different assumptions were made to characterise the underlying processes of diversity dynamics. While the proceeding of ecological theory historically departed from generalisations originating from specialised contexts and from there aiming towards a broader validity, current understanding intends to bring together different views and integrate them into a more global picture.

The argumentation of De Wit goes back to a primary source of the 1930ies that focused on the view that microbiota with more or less any physiological property can be assumed to be present practically everywhere. Then the local environment largely influences which species come to flourish and interact and can become dominant under the prevailing conditions. For larger, multicellular organisms on the other hand, limitations resulting from dispersal probabilities play a considerably larger role and restrict or delay local occurrences.

The paper under review puts forward the emphasis that influences on diversity dynamics result from different statistical frequencies. This is plausible – individual numbers of microbiota are several orders of magnitude higher than the ones of macrobiota in comparable environments. This has obvious implications. The integrative view connects to biogeographic aspects and relates to the well-established Theory of Biogeography for macrobiota, which balances distance-dependent arrival probabilities with extinction probabilities.

In order to drive the approach a bit further (which might go a bit beyond the focus of the current paper), not only biogeographic aspects should be integrated but also the aspect of ecological succession, which is only implicitly addressed in De Wit’s paper. He refers to “niche construction” as a result of species interaction. This process is usually considered as facilitation in succession studies and theory. It might be useful to connect De Wits view also to the theory of ecological succession.

One more step forward in ecological theory integration would be to take a look also at the current results with regard to multiple stability (alternative stable states) and regime shifts in ecological systems as additionally relevant for diversity considerations. Empirical evidence was brought up by studies of Marten Scheffer for shallow lakes (algae dominated versus macrophyte dominated) and was continued meanwhile in quite a number of empirical studies in various environments. A generalisation of this approach is rather interesting also for the interpretation of microbial systems: An example: Drastic changes in the composition of microorganisms present in digestive tracts can well be interpreted as a regime shift between multiple stable states: Diseases like Morbus Crohn and a few others, or problems with Clostridium difficile can be cured by fecal transfusion. This therapeutic intervention is well interpretable as the induction of a transition towards an alternative stable state in a bacterial interaction network (with changes in resulting niche constructions).

Integrative views towards an understanding and interpretation of the processes that govern the species composition in given locations could also refer to debates of the appropriateness of the community concept (that emphasises mutual dependence of organisms) on the one side and the assemblage concepts (that emphasises more stochastic influences and relative independence of species) that was put forward in aquatic marine contexts.

These aspects would be interesting for a discussion of a further unification in ecological theory. This goes beyond of what the author focuses on, however, it may give some hints in which context the study under review is located. A reasonable potential can be seen to go further in an integrative direction in ecological theory dynamics.

If the author would like a further exchange, he is welcome to contact the reviewer.

 

The paper as it is can be well qualified as a valid contribution to theory formation. There are only minor aspects that require correction:

 

Line 60 incorrect : Krieg-swehrmachtgefängnis
Correct: Kriegs-wehrmachtgefängnis

 

Line 163: „For a microbial ecologists …“ should become “For microbial ecologists …”

 

Line 184: Table 1 should be referred to in the text before it occurs in the layout

 

Line 197: Fig. 1 should be referred to in the text before it occurs in the layout

Author Response

Comment 1: In order to drive the approach a bit further (which might go a bit beyond the focus of the current paper), not only biogeographic aspects should be integrated but also the aspect of ecological succession, which is only implicitly addressed in De Wit’s paper. He refers to “niche construction” as a result of species interaction. This process is usually considered as facilitation in succession studies and theory. It might be useful to connect De Wits view also to the theory of ecological succession.

One more step forward in ecological theory integration would be to take a look also at the current results with regard to multiple stability (alternative stable states) and regime shifts in ecological systems as additionally relevant for diversity considerations.

Reply1: I thank the reviewer for his positive comments and interesting suggestions of linking the theory to phenomena as ecological succession and multiple stable state theories. This could be accommodated by adding a further small addition to the Thakur and Wright’s model, i.e. considering that biotic impacts on the environmental filter not only allow selecting new species, but also that the impact could result in the reverse, i.e. a formerly selected species becomes counter selected = filtered out. Therefore, I have added a new Figure (Fig. 3) and expanded the text explaining and mentioning these links. For the objectives described at the end of the Introduction I have also added “This novel framework can be further modified to accommodate for studies of succession and other phenomena, like multiple stable states, which are all based on assuming strong feedbacks of the biocoenosis on the environmental filter.” However, I did not develop all this in great detail as this would indeed reach beyond the scope of this paper. I am available and look forward to discuss these issues directly with the reviewer. As a result of these additions, I have also added the pertinent references.

Comment 2: Four minor aspects that require correction:

Reply2: Done

Reviewer 2 Report

Comments and Suggestions for Authors

This is an interesting manuscript centered on the long-lasting debate of “environmental selection” vs “environmental filtering” in community ecology, specifically focusing on microbial communities. In this short review, the history of the subject is presented in detail starting from Baas Becking’s ubiquity theory. The author presents the elements that explain the divide among microbial and macrobial ecology and discusses Thakur and Wright’s recent conceptual scheme on the subject as well as the practical difficulties regarding microbial community ecology. Thus, the suggestion of small adaptation on Thakur and Wright’s model at the end of the text is interesting and makes sense, although it remains to be seen after being applied, due to the complexities especially regarding the contribution of the host macro-organisms to modifying the environmental filtering.

The manuscript is very well written and the structure is solid. This is very important, especially for a review which focuses on a not very broad subject. In this case, the application of both theories in microbial ecology is easily understood even by someone who is not relevant to the subject.  

I find this manuscript suitable for publication in its present form.  

 

Minor notes:

L120: ecologists

L137: example was

L163: For a microbial ecologist,

L214: Nevertheless,

L225-226: It is a fact that the bacterial code requests pure cultures of living cells for species descriptions.

 

 

 

 

Author Response

General remark: I thank the reviewer for his positive comments and careful reading. Following discussion with the other reviewer, I have added another addition to the Thakur and Wright’s model, i.e. considering that biotic impacts on the environmental filter not only allow selecting new species, but also that the impact could result in the reverse, i.e. a formerly selected species becomes counter selected = filtered out. Therefore, I have added a new Figure (Fig. 3) and expanded the text explaining and mentioning that this allows for accommodating phenomena as ecological succession and multiple stable state theories.

 

Comment: Fiver minor notes all corrected