Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem

Abstract

Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions.

Methylphosphonate metabolism by Pseudomonas sp. populations contributes to the methane oversaturation paradox in an oxic freshwater lake

“…Community composition at all depths was generally consistent with what is normally encountered in freshwater lakes (Newton et al, 2011). Phylum distribution patterns with depth were roughly similar to those described by Preheim et al (2016), although the thermocline depths examined in our study were not the same and so direct comparisons are difficult. Proportional distribution patterns for the major phyla were similar (Fig.…”

“…Phylum distribution patterns with depth were roughly similar to those described by Preheim et al . (), although the thermocline depths examined in our study were not the same and so direct comparisons are difficult. Proportional distribution patterns for the major phyla were similar (Fig.…”

Persistence of bubble outlets in soft, methane‐generating sediments

“…The fine‐scale spatial and temporal concentration of bubble releases implies that the atmospheric methane flux is indeed moderated by the physics of gas bubble generation and mobilization within the sediments. This work motivates further study into the impact of multiple bubble releases on bubble rise and methane dissolution into the water column, and a better‐refined picture of methane delivery is expected to improve our understanding of the biogeochemical cycles at play in these dynamic environments [ Preheim et al , ] and the role that lakes play in the greenhouse effect.…”

Vertical transport of sediment-associated metals and cyanobacteria by ebullition in a stratified lake

“…UML in Arlington, MA is an urban, dimictic kettle lake with an average depth of 15 m, a maximum depth of 24 m, and a surface area of 0.58 km 2 . The lake is used extensively for recreational and scientific purposes, and previous studies have characterized several aspects of methane ebullition (Delwiche and Hemond, 2017;Scandella et al, 2016;Varadharajan and Hemond, 2012) and microbial community structure and function (Preheim et al, 2016;Arora-Williams et al, 2018).…”

“…On 26 June 2018 we sampled for cyanobacteria bubble transport using similar procedures, except we used a simple inverted funnel instead of a custom bubble size sensor to intercept rising bubbles. The sampling funnel was placed 10 m 135 below the water surface, where cyanobacteria concentrations were expected to be lower than the surface based on previous observations (Preheim et al, 2016) to reduce sample contamination with cyanobacteria from the surrounding water column.…”