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Summary: Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross‐disciplinary integration of high‐resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high‐throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N‐cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single‐cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2O production and consumption will respond to future environmental conditions. [ABSTRACT FROM AUTHOR]

The article presents considerations for effective synbiotics design and opportunities for economic development in probiotics. It mentions that the market for probiotics is probably to increase and marketing of the organisms might extend beyond digestive diseases. It states that next-generation probiotics need to have some demonstrated health impact, based on either animal studies or clinical trials in humans.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales. [ABSTRACT FROM AUTHOR]

The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health. Zoo Biol. 34:360-367, 2015. © 2015 Wiley Periodicals Inc. [ABSTRACT FROM AUTHOR]

See also the Commentary by Powell and Sikes [ABSTRACT FROM AUTHOR]

Summary 1. Disturbance is assumed to be a major driver of plant community composition, but whether similar processes operate on associated soil microbial communities is less known. Based on the assumed trade-off between disturbance tolerance and competiveness, we hypothesize that a severe disturbance applied within a semi-natural grassland would shift the arbuscular mycorrhizal (AM) fungal community towards disturbance-tolerant fungi that are rare in undisturbed soils. 2. We used 454-sequencing of the large subunit rDNA region to characterize AM fungal communities in Plantago lanceolata roots grown in the field for 4 months and exposed either to no disturbance or to severe disturbance where fungi from undisturbed soil were either permitted or prevented from re-colonizing the disturbed area. This allowed for a distinction between AM fungi that survived the disturbance and those that quickly re-colonized after a disturbance. To identify AM fungi that could potentially colonize the experimental plants, we also analysed roots from adjacent, undisturbed vegetation. 3. We found 32 fungal operational taxonomic units (OTUs) distributed across five known AM fungal families. Contrary to our expectations, disturbance did not significantly alter the community composition and OTU richness. Instead, OTU abundances were positively correlated across treatments; i.e., common OTUs in undisturbed soil were also common after the severe disturbance. However, the distribution of OTUs within and between plots was largely unpredictable, with approximately 40% of all sequences within a sample belonging to a single OTU of varying identity. The distribution of two plant species that are often poorly colonized by AM fungi ( Dianthus deltoides and Carex arenaria) correlated significantly with the OTU composition, which may indicate that host quality could be an additional driver of fungal communities. 4. Synthesis. Our results suggest that factors other than disturbance drive the relative abundance of OTUs in this grassland and question the long-held assumption that communities shift in a predictable manner after a disturbance event. The reassembly of this fungal community indicates a high community resilience, but substantial local stochasticity and dominance by single OTUs, which could be due to priority effects among abundant AM fungi possessing a similar - and high - degree of disturbance tolerance. [ABSTRACT FROM AUTHOR]