Modelling spatial patterns in host-associated microbial communities

Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.     

The role of Rubisco and cell walls in the interspecific variation in photosynthetic capacity

Photosynthetic capacity is known to vary considerably among species. Its physiological cause and ecological significance have been one of the most fundamental questions in plant ecophysiology. We studied the contents of Rubisco (a key enzyme of photosynthesis) and cell walls in leaves of 26 species with a large variation in photosynthetic rates. We focused on photosynthetic nitrogen-use efficiency (PNUE, photosynthetic rate per nitrogen), which can be expressed as the product of Rubisco-use efficiency (RBUE, photosynthetic rate per Rubisco) and Rubisco nitrogen fraction (RNF, Rubisco nitrogen per total leaf nitrogen). RBUE accounted for 70% of the interspecific variation in PNUE. The variation in RBUE was ascribed partly to stomatal conductance, and other factors such as mesophyll conductance and Rubisco kinetics might also be involved. RNF was also significantly related to PNUE but the correlation was relatively weak. Cell wall nitrogen fraction (WNF, cell wall nitrogen per total leaf nitrogen) increased with increasing leaf mass per area, but there was no correlation between RNF and WNF. These results suggest that nitrogen allocation to cell walls does not explain the variation in PNUE. The difference in PNUE was not caused by a sole factor that was markedly different among species but by several factors each of which was slightly disadvantageous in low PNUE species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.