The Ocean....from the microscale
At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment. New technologies, including microfluidics, high-speed video-microscopy and image analysis, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology. I will illustrate this 'natural history approach to microbial ecology' by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) direct evidence for a diverse gallery of microscale microbial hotspots in the ocean; (ii) a new framework for understanding the evolution of microbial diversity in the ocean; and (iii) microfluidic experiments to capture the dramatic chemotactic abilities of bacterial pathogens towards the roiling surface of coral hosts. Through these examples, I hope to show that direct visualization can foster a new layer of understanding in microbial ecology and can help us unlock the ocean's microscale.
Organic phosphorus acquisition may be a functional driver of community structure for ectomycorrhizal fungi in a tri-partite symbiosis
Alnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria, and while their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts. We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus and nitrogen as compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii. At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than those from P. menziesii, while potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites. At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host. Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic phosphorus acquisition abilities relative to non-Frankia ECM hosts. This shift, in combination with chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities.
Metal(loid) bioaccessibility dictates microbial community composition in acid sulfate soil horizons and sulfidic drain sediments
Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically-disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing. Diversity analyses were problematic due to the high microbiological heterogeneity between each geochemical replicate. Taxonomic analyses combined with measurements of metal(loid) bioaccessibility identified significant correlations to genera (5 % phylogenetic distance) abundances. A number of correlations between genera abundance and bioaccessible Al, Cr, Co, Cu, Mn, Ni, Zn, and As concentrations were observed, indicating that metal(loid) tolerance influences microbial community compositions in these types of landscapes. Of note, Mn was highly bioaccessible (≤ 24 % total soil Mn); and Mn bioaccessibility positively correlated to Acidobacterium abundance, but negatively correlated to Holophaga abundance and two unidentified archaeal genera belonging to Crenarchaeota were also correlated to bioaccessible Mn concentrations, suggesting these genera can exploit Mn redox chemistry.
Another great JAMS evening at the Australian Museum. Nicolas Barraud from UNSW kicked off with a biotechnology story about the use of nitric oxide in biofilm control. John-Sebastien Eden from Eddie Holmes group at USyd gave us the low down on norovirus evolution using the Sydney 2012 strain (the chunder from downunder) as a case study. Somehow our two 15 min presentations consumed an hour so starting back late after the break JAMS co-founder Prof Andrew Holmes gave an excellent presentation on what shapes microbial communities in the the gut. Despite the late start Andy had the audience glued to their seats with a showcase of technology used to unravel human-gut microbiome interactions.