Effect of Thermal Hydrolysis Pretreatment on Anaerobic Digestion of Protein-Rich Biowaste: Process Performance and Microbial Community Structures Shift

To reveal the effects of thermal hydrolysis (TH) pretreatment (THPT) on anaerobic digestion (AD) of protein-rich substrates, discarded tofu was chosen as the object, and its batch AD tests of tofu before and after being subjected to TH at gradually increasing organic loads were carried out and the AD process characteristics were compared; furthermore, its continuous AD tests without and with THPT were also conducted and the difference of the microbial community structures was investigated. The results showed that, during AD of protein-rich tofu with increase in the organic load, inhibition from severe acidification prior to accumulation of ammonia nitrogen (AN) occurred. THPT helped overcome the acidification inhibition present in batch AD of tofu at such a high TS content of 3.6%, to obtain the maximum methane yield rate of 589.39 ml·(gVS)−1. Continuous AD of protein-rich tofu heavily depended on ammonia-tolerant hydrogenotrophic methanogens and bacteria. The continuous AD processes acclimated by HT substrates seemed to be resistant to severe organic loads, by boosting growth of ammonia-tolerant microorganisms, above all methylotrophic methanogens such as the genera RumEnM2 and methanomassiliicoccus. The process response of continuous AD of HT tofu was hysteretic, suggesting that a sufficiently long adaptation period was required for stabilizing the AD system.

Dietary Supplementation throughout Life with Non-Digestible Oligosaccharides and/or n-3 Poly-Unsaturated Fatty Acids in Healthy Mice Modulates the Gut–Immune System–Brain Axis

The composition and activity of the intestinal microbial community structures can be beneficially modulated by nutritional components such as non-digestible oligosaccharides and omega-3 poly-unsaturated fatty acids (n-3 PUFAs). These components affect immune function, brain development and behaviour. We investigated the additive effect of a dietary combination of scGOS:lcFOS and n-3 PUFAs on caecal content microbial community structures and development of the immune system, brain and behaviour from day of birth to early adulthood in healthy mice. Male BALB/cByJ mice received a control or enriched diet with a combination of scGOS:lcFOS (9:1) and 6% tuna oil (n-3 PUFAs) or individually scGOS:lcFOS (9:1) or 6% tuna oil (n-3 PUFAs). Behaviour, caecal content microbiota composition, short-chain fatty acid levels, brain monoamine levels, enterochromaffin cells and immune parameters in the mesenteric lymph nodes (MLN) and spleen were assessed. Caecal content microbial community structures displayed differences between the control and dietary groups, and between the dietary groups. Compared to control diet, the scGOS:lcFOS and combination diets increased caecal saccharolytic fermentation activity. The diets enhanced the number of enterochromaffin cells. The combination diet had no effects on the immune cells. Although the dietary effect on behaviour was limited, serotonin and serotonin metabolite levels in the amygdala were increased in the combination diet group. The combination and individual interventions affected caecal content microbial profiles, but had limited effects on behaviour and the immune system. No apparent additive effect was observed when scGOS:lcFOS and n-3 PUFAs were combined. The results suggest that scGOS:lcFOS and n-3 PUFAs together create a balance—the best of both in a healthy host.

Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain)

The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers’ ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.

A Reference Map of Microbiome Composition in Crop Production Across 8 Chinese Provinces

Background: Although microbiome profiling of crop leaves is a relatively new research area, we know that leaf microorganism communities affect the leaf chemical composition, promote growth, and confer protection against deleterious microbes.Results: Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from plants grown at 26 locations in 8 Chinese provinces. After analyzing leaf microbial communities and identifying 4,473 operational taxonomic units (OTU) representing 1,234 species, we obtained a national core microbiome with 14 OTU representing 9 species, with functions for processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. Although there are no obvious impacts from single environmental factors (e.g., temperature, precipitation), there are significant differences in microbial community structures among provinces and clear clustering by region. Finally, LEfSe analysis screened the significantly different species between different sampling locations.Conclusions: Our study demonstrates that both climactic and industrial factors drive microbial diversity on crop plant leaves, and many potentially useful functional bacterial resources present on tobacco leaves are still waiting for harnessing for a variety of bioprocess, agricultural, and environmental detoxification applications.

Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites

Plant associated microbiomes are known to confer fitness advantages to the host. Understanding how plant factors including biochemical traits influence host associated microbiome assembly could facilitate the development of microbiome-mediated solutions for sustainable plant production. Here, we examined microbial community structures of a set of well-characterized Arabidopsis thaliana mutants disrupted in metabolic pathways for the production of glucosinolates, flavonoids, or a number of defense signalling molecules. A. thaliana lines were grown in a natural soil and maintained under greenhouse conditions for 4 weeks before collection of roots for bacterial and fungal community profiling. We found distinct relative abundances and diversities of bacterial and fungal communities assembled in the individual A. thaliana mutants compared to their parental lines. Bacterial and fungal genera were mostly enriched than depleted in secondary metabolite and defense signaling mutants, except for flavonoid mutations on fungi communities. Bacterial genera Azospirillum and Flavobacterium were significantly enriched in most of the glucosinolate, flavonoid and signalling mutants while the fungal taxa Sporobolomyces and Emericellopsis were enriched in several glucosinolates and signalling mutants. Whilst the present study revealed marked differences in microbiomes of Arabidopsis mutants and their parental lines, it is suggestive that unknown enzymatic and pleiotropic activities of the mutated genes could contribute to the identified host-associated microbiomes. Notwithstanding, this study revealed interesting gene-microbiota links, and thus represents valuable resource data for selecting candidate A. thaliana mutants for analyzing the links between host genetics and the associated microbiome.

Fungi Dominated the Incorporation of 13C-CO2 into Microbial Biomass in Tomato Rhizosphere Soil under Different CO2 Concentrations

An elevated CO2 (eCO2) fumigation experiment was carried out to study the influence of various CO2 concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol−1 CO2 fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of 13C-PLFAs was much higher under eCO2 treatment. Most of the 13C-CO2 was incorporated into the 13C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G−) and i17:0 (Gram-positive bacteria, G+) via rhizodeposition from tomato under ambient CO2 (aCO2) and eCO2 treatments, suggesting similar responses of active microorganisms to different CO2 treatments. However, the fungi (characterized by the 13C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO2. Actinomycetes, marked by the 13C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO2 treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO2 significantly affected microbial biomass and microbial community structures involved in the incorporation of 13C-CO2 via tomato root secretions, as supported by Adonis analysis and the Mantel test.