State Of Microbial Communities Research Articles

Hysteretic and asynchronous regime shifts of bacterial and micro-eukaryotic communities driven by nutrient loading

Nutrient pollution is pervasive in many urban rivers, while restoration measures that reduce nutrient loading but fail to improve biological communities often lack effectiveness due to the indispensable role of biota, especially multi-taxa, in enhancing ecosystem stability and function. The investigation of the response patterns of multi-taxa to the nutrient loading in urban rivers is important for the recovery of biota structure and thus ecosystem function. However, little is known about the response patterns of multi-taxa and their impact on ecosystem structure and function in urban rivers. Here, the study, from the perspective of alternative stable states theory, showed the hysteretic response of both bacterial and micro-eukaryotic communities to nutrient loading based on the field investigation and environmental DNA metabarcoding. Bistability was shown to exist in both bacterial and micro-eukaryotic communities, demonstrating that the response of microbiota to nutrient loading was a regime shifts with hysteresis. Potential analysis then indicated that the increased nutrient loading drove regime shifts in the bacterial community and the micro-eukaryotic community towards a state dominated by anaerobic bacteria and benthic Bacillariophyta, respectively. High nutrient loading was found to reduce the relative abundance of metazoan, but increase that of eukaryotic algae, which made the trophic pyramid top-lighter and bottom-heavier, probably exacerbating the degradation of ecosystem function. It should be noted that, in response to the reduced nutrient loading, the recovery threshold of micro-eukaryotic communities (nutrient loading = ∼0.5) was lower than that of bacterial communities (nutrient loading = ∼1.2), demonstrating longer hysteresis of micro-eukaryotic communities. In addition, the markedly positive correlation between the status of microbial communities and N-related enzyme activities suggested the recovery of microbial communities probably will benefit the improvement of N-cycling functionality. The obtained results provide a deep insight into the collapse and recovery trajectories of multi-trophic microbiota to the nutrient loading gradient and their impact on the N transformation potential, therefore benefiting the restoration and management of urban rivers.

Linkage between Leaf–Litter–Soil, Microbial Resource Limitation, and Carbon-Use Efficiency in Successive Chinese Fir (Cunninghamia lanceolata) Plantations

Chinese fir (Cunninghamia lanceolata) is a kind of evergreen coniferous tree species, the expansion of its pure forest area and multiple generations of continuous planting has led to a decline of stand quality and woodland fertility. To further investigate the relationship between leaf, litter, and soil stoichiometry, microbial community status, and microbial resource limitation of Chinese fir after continuous planting. We studied the C, N, and P stoichiometries of leaf, litter, and soil from successive rotations of Chinese fir plantations. In addition to this, soil microbial biomass C, N, and P, extracellular enzymes, as well as the soil microbial community composition, were determined. The continuous planting of Chinese fir significantly increased the leaf N and P contents and decreased the C content of litter, and the soil C:N and C:P ratios, thus leading to a soil stoichiometric imbalance. The continuous planting of Chinese fir plantations significantly increased the soil microbial biomass. Compared with the first-generation plantations, the N and P contents of the second- and third-generation plantations increased by 37.11%, 21.83% and 46.28%, 73.38%, respectively, thus alleviating the restriction of microbial N and P. Under continuous planting, the extracellular enzyme activities of N (NAG + LAP) and P (AP) were significantly decreased, and those of the second- and third-generation plantations were significantly decreased by 7.05%, 9.43% and 11.79%, 48.94%, respectively, compared with those of the first-generation plantations, resulting in an increase of 7.85 and 3.19% in carbon-use efficiency. The fungi:bacteria (F:B) ratio of the soil microbial community was elevated in successive plantations. The least squares pathway model (PLS-PM) indicated that the stoichiometric ratio of ecological enzymes had an indirect negative effect on CUE, and was the strongest predictor. This study showed that the successive plantation of Chinese fir resulted in a leaf, litter, and soil stoichiometric imbalance, further affecting community composition and resource limitation of soil microorganisms.

Impact of salt and exogenous AM inoculation on indigenous microbial community structure in the rhizosphere of dioecious plant, Populus cathayana

The sex-specific physical and biochemical responses in dioecious plants to abiotic stresses could result in gender imbalance, and how to ease the current situation by microorganisms is still unclear. Using native soil where poplars were grown, growth parameters, soil physicochemical properties in the rhizosphere soil of different sexes of Populus cathayana exposed to salt stress and exogenous arbuscular mycorrhizal (AM) inoculation were tested. Besides, the sex-specific microbial community structures in the rhizosphere soil of different sexes of Populus cathayana were compared under salt stress. To identify the sex-specific microbial community characteristics related to salinity and AM symbiosis, a combined qPCR and DGGE method was used to monitor microbial community diversity. Seedlings suffered severe pressure by salt stress, reflected in limited growth, biomass, and nutrient element accumulation, especially on females. Exogenous AM inoculation treatment alleviated these negative effects, especially under salt treatment of 75 mM. Compared with salt effect, exogenous AM inoculation treatment showed a greater effect on soil physical–chemical properties of both sexes. Based on DGGE results, salt stress negatively affected fungal richness but positively affected fungal Simpson diversity index, while exogenous AM inoculation treatment showed the opposite effect. Structural equation modeling (SEM) was performed to show the causal relationships between salt and exogenous AM inoculation treatments with biomass accumulation and microbial community: salt and exogenous AM inoculation treatment showed complicated effects on elementary concentrations, soil properties, which resulted in different relationship with biomass accumulation and microbial community. Salt stress had a negative effect on soil properties and microbial community structure in the rhizosphere soil of P. cathayana, whereas exogenous AM inoculation showed positive impacts on most of the soil physical–chemical properties and microbial community status.

Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients.

ABSTRACTSignificant gut microbiota heterogeneity exists among ulcerative colitis (UC) patients, though the clinical implications of this variance are unknown. We hypothesized that ethnically distinct UC patients exhibit discrete gut microbiotas with unique metabolic programming that differentially influence immune activity and clinical status. Using parallel 16S rRNA and internal transcribed spacer 2 sequencing of fecal samples (UC, 30; healthy, 13), we corroborated previous observations of UC-associated bacterial diversity depletion and demonstrated significant Saccharomycetales expansion as characteristic of UC gut dysbiosis. Furthermore, we identified four distinct microbial community states (MCSs) within our cohort, confirmed their existence in an independent UC cohort, and demonstrated their coassociation with both patient ethnicity and disease severity. Each MCS was uniquely enriched for specific amino acid, carbohydrate, and lipid metabolism pathways and exhibited significant luminal enrichment of the metabolic products of these pathways. Using a novel ex vivo human dendritic cell and T-cell coculture assay, we showed that exposure to fecal water from UC patients caused significant Th2 skewing in CD4+ T-cell populations compared to that of healthy participants. In addition, fecal water from patients in whom their MCS was associated with the highest level of disease severity induced the most dramatic Th2 skewing. Combined with future investigations, these observations could lead to the identification of highly resolved UC subsets based on defined microbial gradients or discrete microbial features that may be exploited for the development of novel, more effective therapies.

Functional diversity of microbial communities in saline soils of the semidesert zone

The health status of microbial communities in soils of the Sulak Lowland (Dagestan) was estimated on the basis of data on their functional diversity. The health status of the microbial communities decreased in the following soil sequence: typical meadow soil > meadow-chestnut soil > dark chestnut soil > saline soil (solonchak). The low concentration of soluble salts (<1 meq/100 g of soil) had a positive effect on the functioning of the microbial communities. The health status of the microbial communities also depended on the soil humus content and pH conditions.