Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

Background Soil microorganisms in the thawing permafrost play key roles in the maintenance of ecosystem function and regulation of biogeochemical cycles. However, our knowledge of patterns and drivers of permafrost microbial communities is limited in northeastern China. Therefore, we investigated the community structure of soil bacteria in the active, transition and permafrost layers based on 90 soil samples collected from 10 sites across the continuous permafrost region using high-throughput Illumina sequencing. Results Proteobacteria (31.59%), Acidobacteria (18.63%), Bacteroidetes (9.74%), Chloroflexi (7.01%) and Actinobacteria (6.92%) were the predominant phyla of the bacterial community in all soil layers; however, the relative abundances of the dominant bacterial taxa varied with soil depth. The bacterial community alpha-diversity based on the Shannon index and the phylogenetic diversity index both decreased significantly with depth across the transition from active layer to permafrost layer. Nonmetric multidimensional scaling analysis and permutation multivariate analysis of variance revealed that microbial community structures were significantly different among layers. Redundancy analysis and Spearman’s correlation analysis showed that soil properties differed between layers such as soil nutrient content, temperature and moisture mainly drove the differentiation of bacterial communities. Conclusions Our results revealed significant differences in bacterial composition and diversity among soil layers. Our findings suggest that the heterogeneous environmental conditions between the three soil horizons had strong influences on microbial niche differentiation and further explained the variability of soil bacterial community structures. This effort to profile the vertical distribution of bacterial communities may enable better evaluations of changes in microbial dynamics in response to permafrost thaw, which would be beneficial to ecological conservation of permafrost ecosystems.

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.

Responses of CO2 Emissions and Soil Microbial Community Structures to Organic Amendment in Two Contrasting Soils in Zambia

In sub-Saharan Africa, efforts have been made to increase soil carbon (C) content in agricultural ecosystems, due to severe soil degradation. The use of organic materials is one of the realistic methods to recover soil C. However, the impacts of organic amendments on soil microbial community and C cycles under limited soil C conditions are still unknown. We conducted field experiments using organic amendments in two sites with contrasting C content in Zambia. At both sites, temporal changes of soil carbon dioxide (CO2) emissions, bacterial and archaeal community structures were monitored during crop growing season (126 days). The organic amendments increased CO2 emissions with increased bacterial and archaeal abundance in the Kabwe site, while no impacts were shown in the Lusaka site. We also observed larger temporal variability in soil microbial community structure in Kabwe than in Lusaka. These contrasting results between the two soils might be due to the gap in microbial community stability. However, organic amendments have a significant potential to enhance microbial abundance and consequently sequester soil C in the Kabwe site. Site-specific strategies are needed to deal with the issues of soil C depletion in drylands.