Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome

Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin bio-synthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula x Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies

Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high resolutioncommunity profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula x Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non target DNA and retrieval of bacterial OTUs

Paul Eelen : reflections on life and work

This manuscript is part of a special issue to commemorate professor Paul Eelen, who passed away on August 21, 2016. Paul was a clinically oriented scientist, for whom learning principles (Pavlovian or operant) were more than salivary responses and lever presses. His expertise in learning psychology and his enthusiasm to translate this knowledge to clinical practice inspired many inside and outside academia. Several of his original writings were in the Dutch language. Instead of editing a special issue with contributions of colleagues and friends, we decided to translate a selection of his manuscripts to English to allow wide access to his original insights and opinions. Even though the manuscripts were written more than two decades ago, their content is surprisingly contemporary. This introductory article presents a reflection on Paul’s career and legacy and introduces the selected manuscripts that are part of this special issue

The loss of prediction in extinction: The 'neglected’ rise of contextual anxiety

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Dopamine: From prediction error to psychotherapy

Dopamine, one of the main neurotransmitters in the mammalian brain, has been implicated in the coding of prediction errors that govern reward learning as well as fear extinction learning. Psychotherapy too can be viewed as a form of error-based learning, because it challenges erroneous beliefs and behavioral patterns in order to induce long-term changes in emotions, cognitions and behaviors. Exposure therapy, for example, relies in part on fear extinction principles to violate erroneous expectancies of danger and induce novel safety learning that inhibits and therefore reduces fear in the long term. As most forms of psychotherapy, however, exposure therapy suffers from non-response, dropout and relapse. This narrative review focuses on the role of midbrain and prefrontal dopamine in novel safety learning and investigates possible pathways through which dopamine-based interventions could be used as an adjunct to improve both the response and the long term effects of the therapy. Convincing evidence exists for an involvement of the midbrain dopamine system in the acquisition of new, safe memories. Additionally, prefrontal dopamine is emerging as a key ingredient for the consolidation of fear extinction. We propose that applying a dopamine Prediction Error perspective to psychotherapy can inspire both pharmacological and non-pharmacological studies aimed at discovering innovative ways to enhance the acquisition of safety memories. Additionally, we call for further empirical investigations on dopamine-oriented drugs that might be able to maximize consolidation of successful fear extinction and its long-term retention after therapy, and we propose to also include investigations on non-pharmacological interventions with putative prefrontal dopaminergic effects, like working memory training.status: publishe

What a relief! The pleasure of threat avoidance

Relief, a pleasurable experience, is often triggered by successful threat avoidance. Although relief is regarded as the positive reinforcer for avoidance behavior, its rewarding nature remains to be demonstrated. In our study, fifty participants responded to cues associated with different magnitudes of monetary values or electrical stimuli. Successful responses to those cues resulted in monetary gains (i.e., rewards) or omissions of electrical stimulation (i.e., relief), followed by a pleasantness rating scale. We also measured physiological arousal via skin conductance. As expected, we found that for reward and relief similarly, higher magnitudes elicited more successful responses, higher pleasantness ratings, and higher skin conductance responses. Moreover, differential reward/relief response patterns predicted later choices between reward and relief cues. These findings indicate that relief induced by threat omissions is functionally equivalent to receiving a reward, confirming that relief is a positive reinforcer for threat avoidance behaviors, which provides a new theoretical perspective on the learning process of active threat avoidance

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