Using molecular microbial ecology to define differential responses to the inoculation of barley silage

Previously, we investigated the impact of a mixed Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus casei inoculant on fermentation and aerobic stability of barley silage over two years in 2009 and 2010. In 2009, a classical response to inoculation was obtained with an increase in acetic acid concentration of silage ensiled in both mini- and bag silos. In 2010, this classical response was not observed in mini-silos but was observed in bag silos. The objective of this study was to determine if molecular microbial ecology could explain the differential responses to the inoculation of barley silage between the two years. The Illumina MiSeq sequencing results showed that inoculation increased Lactobacillus and lowered Pediococcus, Weissella, and Leuconostoc in both types of silos in 2009. However, a similar trend was not observed in mini-silos, but was instead observed in bag silos in 2010. Inoculation did not alter the core fungal community in either silo type in either year. Cladosporium, Leptosphaeria, and Cryptococcus were abundant in fresh forage, but were superseded by Pichia and Kazachstania after ensiling. Our results suggest that changes in silage chemistry corresponded to differences observed in microbial ecology. Inoculation may have less impact when using more mature crops with shorter ensiling times.

Towards safer stable isotope probing — effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.

Permeable reactive interceptors: blocking diffuse nutrient and greenhouse gases losses in key areas of the farming landscape

SUMMARYEngineered remediation technologies such as denitrifying bioreactors target single contaminants along a nutrient transfer continuum. However, mixed contaminant discharges to a water body are more common from agricultural systems. Indeed, evidence presented herein indicates that pollution swapping within denitrifying bioreactor systems adds to such deleterious discharges. The present paper proposes a more holistic approach to contaminant remediation on farms, moving from the use of ‘denitrifying bioreactors’ to the concept of a ‘permeable reactive interceptor’ (PRI). Besides management changes, a PRI should contain additional remediation cells for specific contaminants in the form of solutes, particles or gases. Balance equations and case studies representing different geographic areas are presented and used to create weighting factors. Results showed that national legislation with respect to water and gaseous emissions will inform the eventual PRI design. As it will be expensive to monitor a system continuously in a holistic manner, it is suggested that developments in the field of molecular microbial ecology are essential to provide further insight in terms of element dynamics and the environmental controls on biotransformation and retention processes within PRIs. In turn, microbial and molecular fingerprinting could be used as an in-situ cost-effective tool to assess nutrient and gas balances during the operational phases of a PRI.