Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates.

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport.

Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater.

Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established.

Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats.

Cyanobacteria and extracellular polymeric substances (EPS) in peritidal pustular microbial mats have a two-billion-year-old fossil record. To understand the composition, production, degradation, and potential role of EPS in modern analogous communities, we sampled pustular mats from Shark Bay, Australia and analyzed their EPS matrix. Biochemical and microscopic analyses identified sulfated organic compounds as major components of mat EPS.

Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment.

Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri.

Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in in a Mixed Carbon Medium.

Denitrifying microbes sequentially reduce nitrate (NO ) to nitrite (NO ), NO, NO, and N through enzymes encoded by , , , and . Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NO ) utilization.

Denitrifying bacteria respond to and shape microscale gradients within particulate matrices.

Heterotrophic denitrification enables facultative anaerobes to continue growing even when limited by oxygen (O) availability. Particles in particular provide physical matrices characterized by reduced O permeability even in well-oxygenated bulk conditions, creating microenvironments where microbial denitrifiers may proliferate. Whereas numerical particle models generally describe denitrification as a function of radius, here we provide evidence for heterogeneity of intraparticle denitrification activity due to local interactions within and among microcolonies.

Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages.

Evidence suggests that bacterial community spatial organization affects their ecological function, yet details of the mechanisms that promote spatial patterns remain difficult to resolve experimentally. In contrast to bacterial communities in liquid cultures, surface-attached range expansion fosters genetic segregation of the growing population with preferential access to nutrients and reduced mechanical restrictions for cells at the expanding periphery. Here we elucidate how localized conditions in cross-feeding bacterial communities shape community spatial organization.

Interaction-dependent effects of surface structure on microbial spatial self-organization.

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization.

Bridging the Holistic-Reductionist Divide in Microbial Ecology.

Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of "synthetic" systems and the convolution and complexity of natural environments.