Scaling up: the next challenge in environmental microbiology

Capturing the genetic makeup of the active microbiome in situ

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Ecology and physics of bacterial chemotaxis in the ocean

Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as "high performance" compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean. These fast responses are advantageous in a broad range of ecological processes, including attaching to particles, exploiting particle plumes, retaining position close to phytoplankton cells, colonizing host animals, and hovering at a preferred height above the sediment-water interface. At larger scales, these responses can impact ocean biogeochemistry by increasing the rates of chemical transformation, influencing the flux of sinking material, and potentially altering the balance of biomass incorporation versus respiration. This review highlights the physical and ecological processes underpinning bacterial motility and chemotaxis in the ocean, describes the current state of knowledge of chemotaxis in marine bacteria, and summarizes our understanding of how these microscale dynamics scale up to affect ecosystem-scale processes in the sea.

An environment-sensitive synthetic microbial ecosystem

Microbial ecosystems have been widely used in industrial production, but the inter-relationships of organisms within them haven't been completely clarified due to complex composition and structure of natural microbial ecosystems. So it is challenging for ecologists to get deep insights on how ecosystems function and interplay with surrounding environments. But the recent progresses in synthetic biology show that construction of artificial ecosystems where relationships of species are comparatively clear could help us further uncover the meadow of those tiny societies. By using two quorum-sensing signal transduction circuits, this research designed, simulated and constructed a synthetic ecosystem where various population dynamics formed by changing environmental factors. Coherent experimental data and mathematical simulation in our study show that different antibiotics levels and initial cell densities can result in correlated population dynamics such as extinction, obligatory mutualism, facultative mutualism and commensalism. This synthetic ecosystem provides valuable information for addressing questions in ecology and may act as a chassis for construction of more complex microbial ecosystems.

PCR-denaturing gradient gel electrophoresis of complex microbial communities: a two-step approach to address the effect of gel-to-gel variation and allow valid comparisons across a large dataset

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis software package (TL120 v2006, Phoretix 1D Advanced) followed by a simple interpolation step in Matlab minimized the effect of gel-to-gel variation, allowing for comparisons between large numbers of samples with a high degree of confidence. At the same time, data were obtained in the form of whole densitometric curves, rather than as band presence/absence or intensity information, and could be readily analyzed by a collection of well-established multivariate methods. This work clearly demonstrates that there is still room for significant improvements as to the way large DGGE datasets are processed and statistically interrogated.

Use of multivariate statistics for 16S rRNA gene analysis of microbial communities

Understanding dynamic processes and diversity in microbial communities is of key importance for combating pathogens and for stimulating beneficial bacteria. We have addressed these challenges utilising multivariate statistics for analyses of microbial community structures. We based our microbial community analyses on 16S rRNA gene data. This gene is by far the most widely applied genetic marker for phylogenetic and microbial community studies. Both probe and clone library data were analysed. We analysed the clone library data using a newly developed coordinate-based phylogenetic approach. By using coordinates, we avoid both DNA sequence alignments and the need for definition of operational taxonomic units (OTUs). The basic principle is to transform the sequence data to frequencies of multimers (short sequences of n=2 to 6), and then to use principal component analyses (PCA) for data compression into an orthogonal coordinate space. We used our coordinate method for global 16S rRNA gene analyses of prokaryotes. When comparing microbial communities, it is often important to determine the relationship between the microflora and knowledge about the samples analysed. We used partial least square regression (PLSR) to relate physical/chemical properties to microbial community composition. This was done by analysing both probe and clone library data using the effect of modified atmosphere packaging (MAP) on fish microflora as an example. We are currently investigating approaches to describe dynamic microbial community interactions. Our ultimate goal is to understand and model the main dynamic interactions in complete microbial communities.

Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater⋆

In order to better understand the ecology of microorganisms responsible for secondary production in the Southern Ocean the activity of Flavobacteria communities on diatom detritus in seawater mesocosms was investigated. Seawater was collected from different parts of the Southern Ocean including the Polar Front Zone (PFZ), ice-edge area of the Antarctic Zone (AZ), and a site in the AZ ice pack. Detritus from the cosmopolitan marine diatom Nitzschia closterium Ehrenberg was resuspended in mesocosms containing seawater filtered to remove particulate organic matter, including particle-associated bacteria and most eukaryotes, but retaining native planktonic bacterial assemblages. Mesocosms were incubated at 2 degrees C and samples analysed for changes in community composition using denaturing gradient gel electrophoresis (DGGE), real-time PCR and fluorescent in-situ hybridization (FISH). DGGE banding patterns and FISH images demonstrated rapid bacterial colonization of the detritus, dominated by members of class gamma-Proteobacteria, alpha-Proteobacteria and Flavobacteria. Real-time PCR data indicated members of class Flavobacteria were involved in initial colonization of detrital aggregate, however relative abundance stayed at similar levels found for the original native particle-associated populations. 16S rRNA gene DGGE banding patterns and sequence analysis demonstrated significant variation in Flavobacteria community structure occurred in the first 20 days of the experiment before community stabilization occurred. The community structures between the three mesocosms also markedly differed and major colonizers were primarily derived from detectable members of the initial particle-associated Flavobacteria community, however the abundant uncultured Flavobacteria agg58 clone-related and DE cluster 2 clades, previously identified in Southern Ocean seawater were not observed to colonize the detritus.