My recent dabbling and speculation in the world of molecular biology and biochemistry (see “Concentrating on carbon …” and “As if through a glass darkly …”) reawakened deep memories of lectures on protein structure as an undergraduate and, in particular, the different levels at which we understand this. These are:
- Primary structure: the sequence of amino acids in the polypeptide chain;
- Secondary structure: coils and folds along the polypeptide chain caused by hydrogen bonds between peptide groups;
- Tertiary structure: three-dimensional organisation of protein molecules driven by hydrophobic interactions and disulphide bridges; and,
- Quaternary structure: the agglomeration of two or more polypeptide groups to form a single functional unit.
This framework describes journey from the basic understanding of the nature of a protein achieved by Frederick Sanger in the early 1950s, to the modern, ore sophisticated awareness of how the structure determines their mode of action. I remember being particularly taken by a description of how sickle cell anaemia was caused by a change of a single amino acid in the haemoglobin molecule, altering the structure of the protein and, in the process, reducing its capacity to carry oxygen.
There is a metaphor for those of us who study biofilms here. To borrow the analogy of protein structure, the basic list of taxa and their relative abundance is the “primary structure” of a biofilm. Within this basic “name-and-count” we have various “flavours”, from diehard diatomists who ignore all other types of organisms through to those who go beyond counting to consider absolute abundance and cell size in their analyses. Whatever their predilection, however, they share a belief that raw taxonomic information, weighted in some way by quantity, yields enough information to make valid ecological inferences. And, indeed, there are strong precedents for this, especially when the primary goal is to understand broad-scale interactions between biofilms and their chemical environment.
But does this good understanding of the relationship between biofilm “primary structure” and chemistry comes at the expense of a better understanding of the inter-relationships within the biofilm. And, turning that around, might these inter-relationships, in turn, inform a more nuanced interpretation of the relationship between the biofilm and its environment? So let’s push the metaphor with protein structure a little further and see where that leads us.
The “tertiary structure” of a submerged biofilm: this one shows the inter-relationships of diatoms within a Didymosphenia geminata colony. Note how the long stalks of Didymosphenia provide substrates for Achnanthidium cells (on shorter stalks) and needle-like cells of Fragilaria and Ulnaria. You can read more about this here. The image at the top of the post shows a biofilm from the River Wyle, described in more detail here.
We could think of the “secondary structure” of a biofilm as the organisation of cellular units into functional groups. This would differentiate, for example, filaments from single cells, flagellates from non-flagellates and diatoms that live on long stalks from those that live adpressed to surfaces. It could also differentiate cells on the basis of physiology, distinguishing nitrogen-fixers from non-nitrogen fixers, for example. We might see some broad phylogenetic groupings emerging here (motility of diatoms, for example, being quite different from that of flagellated green algae) but also some examples of convergence, where functional groups span more than one algal division.
Quite a few people have explored this, particularly for diatoms, though results are not particularly conclusive. That might be because we cannot really understand the subtleties of biofilm functioning when information on every group except diatoms has been discarded, and it might be because people have largely been searching for broad-scale patterns when the forces that shape these properties work at a finer scale. General trends that have been observed include an increase in the proportion of motile diatoms to increase along enrichment gradients. However, this has never really been converted into a “take-home message” that might inform the decisions that a catchment manager might take, and so rarely form part of routine assessment methods.
Next, there is a “tertiary structure”, the outcome of direct relationships between organisms and environment, interdependencies amongst those organisms to form a three-dimensional matrix, and time. This is the most elusive aspect of biofilm structure, largely because it is invariably destroyed or, at best, greatly distorted during the sample collection and analysis phases. This has been little exploited in ecological studies, perhaps because it is less amenable to the reductive approach that characterises most studies of biofilms. But I think that there is potential here, at the very least, to place the outcomes of quantitative analyses into context. We could, in particular, start to think about the “foundation species” – i.e. those that define the structure of the community by creating locally stable conditions (see the paper by Paul Dayton below). This, in turn, gives us a link to a rich vein of ecological thinking, and helps us to understand not just how communities have changed but also why.
The tertiary structure of a Cladophora-dominated biofilm from the River Team, Co. Durham. Cladophora, in this case, functions as a “foundation species”, creating a habitat within which other algae and microorganisms exist. You can read more about this in “A return to the River Team”.
Finally, if we were looking for a biofilm “quaternary structure” we could, perhaps, think about how the composition at any single point in space and time grades and changes to mould the community to favour fine-scale “patchiness” in the habitat and also to reflect seasonal trends in factors that shape the community (such as grazing). Biofilms, in reality, represent a constantly shifting set of “metacommunities” whose true complexity is almost impossible to capture with current sampling techniques.
Some of this thinking ties in with posts from earlier in the year (see, for example, “Certainly uncertain”, which draws on an understanding of tertiary structure to explain variability in assessments based on phytobenthos communities). But there is more that could be done and I hope to use some of my posts in 2018 to unpick this story in a little more detail.
That’s enough from me for now. Enjoy the rest of the festive season.
Dayton, P. K. (1972). Toward an understanding of community resilience and the potential effects of enrichments to the benthos at McMurdo Sound, Antarctica. pp. 81–96 in Proceedings of the Colloquium on Conservation Problems Allen Press, Lawrence, Kansas.
“secondary structure” of biofilms
Gottschalk, S. & Kahlert, M. (2012). Shifts in taxonomical and guild composition of littoral diatom assemblages along environmental gradients. Hydrobiologia 694: 41-56.
Law, R., Elliott, J.A., & Thackeray, S.J. (2014). Do functional or morphological classifications explain stream phytobenthic community assemblages? Diatom Research 29: 309-324.
Molloy, J.M. (1992). Diatom communities along stream longitudinal gradients. Freshwater Biology, 28: 56-69.
Steinman, A.D., Mulholland, P.J. & Hill, W.R. (1992). Functional responses associated with growth form in stream algae. Journal of the North American Benthological Society 11: 229-243.
“tertiary structure” of biofilms
Bergey, E.A., Boettiger, C.A. & Resh, V.H. (1995). Effects of water velocity on the architecture and epiphytes of Cladophora glomerata (Chlorophyta). Journal of Phycology 31: 264-271.
Blenkinsopp, S.A. & Lock, M.A. (1994). The impact of storm-flow on river biofilm architecture. Journal of Phycology 30: 807-818.
Kelly, M.G. (2012). The semiotics of slime: visual representation of phytobenthos as an aid to understanding ecological status. Freshwater Reviews 5: 105-119.