Grassland degradation is a major ecological problem at present, leading to changes in the grassland environment and the soil microbial community. Here, based on full-length 16S rRNA gene sequencing, we highlight the importance of small-scale environmental changes on the Qinghai-Tibet Plateau grassland for the composition and assembly processes of abundant and rare bacterial taxa. The results showed that grassland vegetation coverage affected the taxonomic and phylogenetic composition of rare bacterial taxa more than abundant bacterial taxa. The taxonomic composition and phylogenetic composition of rare bacterial taxa were also affected by soil nutrients. The relative contribution of deterministic processes (variable selection and homogeneous selection) to rare bacterial taxa was higher than that of the abundant bacterial taxa. The competitive potential within rare bacterial taxa was lower than that of the competitive potential between rare and non-rare bacterial taxa or within non-rare bacterial taxa. The assembly of rare bacterial taxa was more susceptible to environmental changes caused by grassland degradation than the abundant bacterial taxa. Furthermore, the distribution of rare bacterial taxa in the different degraded grassland soil was more local than that of abundant bacterial taxa. Thus, rare bacterial taxa could be considered an ecological indicator of grassland degradation. These findings help to improve our understanding of the composition and assembly mechanism of the bacterial communities in degraded grassland and provide a basis for the establishment of the grassland degradation management strategy.

Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.

In the Tibetan agro-pastoral ecotone, which has an altitude of 4000 m above sea level, small-scale cropland tillage has been exploited on the grassland surrounding the houses of farmers and herdsmen. However, knowledge of the effects of land change from grassland to cropland on soil nutrients and microbial communities is poor. Here, we investigated the structure and assembly mechanism of bacterial communities in cropland (tillage) and grassland (non-tillage) from an agro-pastoral ecotone of Tibet. Results indicated that soil nutrients and composition of bacterial communities changed dramatically in the process of land-use change from grassland to cropland. The pH value and the content of total nitrogen, organic material, total potassium, and total phosphorus in cropland soil were well above those in grassland soil, whereas the soil bulk density and ammonia nitrogen content in grassland soil were higher than those in cropland soil. Proteobacteria (30.5%) and Acidobacteria (21.7%) were the key components in cropland soil, whereas Proteobacteria (31.5%) and Actinobacteria (27.7%) were the main components in grassland soils. Tillage promotes uniformity of bacterial communities in cropland soils. In particular, the higher migration rate may increase the coexistence patterns of the bacterial community in cropland soils. These results also suggest that the tillage promotes the migration and coexistence of bacterial communities in the grassland soil of an agro-pastoral ecotone. In addition, the stochastic process was the dominant assembly pattern of the bacterial community in cropland, whereas, in grassland soil, the community assembly was more deterministic. These findings provide new insights into the changes in soil nutrients and microbial communities during the conversion of grassland to cropland in the agro-pastoral ecotone.