Bacterial community in cold and alkaline environments of Hoh Xil basin in Qinghai–Tibet Plateau and isolation of potential sources of microbiota

Bacterial and archaeal communities within the alkaline soda Langaco Lake in the Qinghai-Tibet Plateau

Purpose

Langaco Lake (LGL) is a soda lake located at an altitude of 4548 m in the Qinghai-Tibet Plateau in China. LGL exhibits unique hydrochemical characteristics among soda lakes, but little is known about the microbial diversity of LGL and the microbial interactions with environmental factors.

Methods

The water samples were filtered using chemical-grade cellulose acetate membrane (pore size of 0.45 μm), and the hydrochemical characteristics were analyzed. Community DNA was extracted, and then high-throughput sequencing of 16S rRNA genes was conducted to evaluate the composition of the microbial community.

Results

The high-throughput sequencing of 16S rRNA genes revealed that the bacterial diversity in LGL consisted of 327 genera in 24 phyla (4871 operational taxonomic units (OTUs); Shannon index values of 5.20–6.07), with a significantly higher diversity than that of the Archaea (eight phyla and 29 genera comprising 1008 OTUs; Shannon index values of 2.98–3.30). The bacterial communities were dominated by Proteobacteria (relative abundances of 42.79–53.70%), followed by Bacteroidetes (11.13–15.18%), Planctomycetes (4.20–12.82%), Acidobacteria (5.91–9.50%), Actinobacteria (2.60–5.80%), and Verrucomicrobia (2.11–4.08%). Furthermore, the archaeal communities were dominated by Crenarchaeota (35.97–58.29%), Euryarchaeota (33.02–39.89%), and Woesearchaeota (6.50–21.57%). The dominant bacterial genus was Thiobacillus (8.92–16.78%), and its abundances were most strongly correlated with the total phosphorus (TP) content, pH value, CO32− concentration, and temperature. The most abundant archaeal genus was Methanoregula (21.40–28.29%), and its abundances were the most highly correlated with the total organic carbon (TOC) content, total salinity (TS), and K+ and Na+ concentrations.

Conclusions

The results of this study provide valuable insights for developing a more comprehensive understanding of microbial diversity in these unique carbonate alkaline environments, as well as a better understanding of the microbial resources on the Qinghai-Tibet Plateau.

Bacterial communities associated with mushrooms in the Qinghai-Tibet Plateau are shaped by soil parameters

Fungi capable of producing fruit bodies are essential food and medicine resources. Despite recent advances in the study of microbial communities in mycorrhizospheres, little is known about the bacterial communities contained in fruit bodies. Using high-throughput sequencing, we investigated the bacterial communities in four species of mushrooms located on the alpine meadow and saline-alkali soil of the Qinghai-Tibet Plateau (QTP). Proteobacteria (51.7% on average) and Actinobacteria (28.2% on average) were the dominant phyla in all of the sampled fairy ring fruit bodies, and Acidobacteria (27.5% on average) and Proteobacteria (25.7% on average) dominated their adjacent soils. For the Agria. Bitorquis, Actinobacteria was the dominant phylum in its fruit body (67.5% on average) and adjacent soils (65.9% on average). The alpha diversity (i.e., Chao1, Shannon, Richness, and Simpson indexes) of the bacterial communities in the fruit bodies were significantly lower than those in the soil samples. All of the fungi shared more than half of their bacterial phyla and 16.2% of their total operational taxonomic units (OTUs) with their adjacent soil. Moreover, NH₄⁺ and pH were the key factors associated with bacterial communities in the fruit bodies and soils, respectively. These results indicate that the fungi tend to create a unique niche that selects for specific members of the bacterial community. Using culture-dependent methods, we also isolated 27 bacterial species belonging to three phyla and five classes from fruit bodies and soils. The strains isolated will be useful for future research on interactions between mushroom-forming fungi and their bacterial endosymbionts.

Salinity and seasonality shaping free-living and particle-associated bacterioplankton community assembly in lakeshores of the northeastern Qinghai-Tibet Plateau

Microorganisms in lakeshore zones are essential for pollution interception and biodiversity maintenance. However, the biogeographic patterns of bacterioplankton communities in lakeshore zones and the mechanisms that driving them are poorly understood. We analyzed the 16 S rRNA gene sequences of particle-associated (PA) and free-living (FL) bacterioplankton communities in the lakeshore zones of 14 alpine lakes in two seasons on Qinghai-Tibet Plateau to investigate the bacterial diversity, composition and assembly processes. Our results revealed that PA and FL bacterioplankton communities were driven by both seasonality and salinity in the lakeshores on Qinghai-Tibet Plateau. Compared to FL bacterioplankton, PA bacterioplankton communities were more susceptible to seasonality than spatial salinity. FL bacterioplankton communities were more salinity constrained than the PA counterpart. Besides, the Stegen null model analyses have validated a quantitative bias on stochastic processes at different spatial scales. At a regional scale, stochasticity was the predominant assembly process in both PA and FL bacterioplankton. While at a subregional scale, dispersal limitation was the main contributor of stochastic processes for PA bacterioplankton in summer and heterogeneous selection was the dominant deterministic processes in winter, whereas the community assembly of FL bacterioplankton was more stochastic processes (i.e., dispersal limitation) dominated in the freshwater type but deterministic process (i.e., heterogeneous selection) increased with increasing salinity. Our study provides new insights into both significant spatiotemporal patterns and distinct assembly processes of PA and FL bacterioplankton in alpine lakeshores on the northeastern Qinghai-Tibet Plateau.

Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau

Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.

Elaeagnus angustifolia can improve salt-alkali soil and the health level of soil: Emphasizing the driving role of core microbial communities

Saline-alkali environments are widely distributed in China and significantly hinder the development of agriculture. This study characterizes the long-term effects of planting Elaeagnus angustifolia (E. angustifolia) on the physical and chemical properties, enzyme activities and microbial community characteristics of saline-alkali soil in the Songnen Plain (1, 2 and 3 years). The results showed that planting E. angustifolia reduced soil pH and electrical conductivity (EC) and increased soil total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (Nni), total potassium (TK), dissolved organic C (DOC), dissolved organic matter (DOM) and available potassium (AK) content and catalase, urease, polyphenol oxidase, phosphatase, sucrase and cellulase enzyme activities, and the results peaked in the 3 year. High-throughput sequencing showed that the bacterial abundance and diversity were as follows (from high to low) y3 > y2 > y1 > CK. E. angustifolia resulted in an increase in the relative abundance of the dominant bacteria. Proteobacteria and Pseudomonas were the major phylum and genus, respectively. Redundancy analysis showed that changes in the soil microbial community significantly affect the physical and chemical properties of the soil, with Proteobacteria members being the key microorganisms that reduce soil salinity. Network analysis showed that Pseudomonas (Proteobacteria) participated in the synthesis of key soil enzymes. 16S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, acsB, Pcc and accA) and nitrogen (amoA/B, nxrA, hao, gdh, ureC and nosZ) transformation increased, and Pseudomonas members were key regulators of carbon and nitrogen dynamics. In conclusion, the planting of E. angustifolia could improve the physical and chemical properties of the soil by releasing root exudates into the soil and increasing the diversity and richness of soil microbial communities to improve saline-alkali soil, providing a theoretical basis for improving saline-alkali soil and promoting the sustainable development of modern agriculture.