Bacterial Communities in Stream Biofilms in a Degrading Grassland Watershed on the Qinghai-Tibet Plateau

Rare bacterial biosphere is more environmental controlled and deterministically governed than abundant one in sediment of thermokarst lakes across the Qinghai-Tibet Plateau

Thermokarst lakes are widely distributed in cold regions as a result of ice-rich permafrost thaw. Disentangling the biogeography of abundant and rare microbes is essential to understanding the environmental influences, assembly mechanisms, and responses to climate change of bacterial communities in thermokarst lakes. In light of this, we assessed the abundant and rare bacterial subcommunities in sediments from thermokarst lakes across the Qinghai-Tibet Plateau (QTP). The operational taxonomic unit (OTU) richness was more strongly associated with location and climate factors for abundant subcommunities, while more strongly associated with physicochemical variables for rare subcommunities. The relative abundance of abundant and rare taxa showed opposite patterns with abundant taxa having greater relative abundance at higher latitude and pH, but at lower mean annual precipitation and nutrients. Both the abundant and rare subcommunities had a clear distribution pattern along the gradient of latitude and mean annual precipitation. Abundant subcommunities were dominantly shaped by dispersal limitation processes (80.9%), while rare subcommunities were shaped almost equally by deterministic (47.3%) and stochastic (52.7%) processes. The balance between stochastic and deterministic processes was strongly environmentally adjusted for rare subcommunities, while not associated with environmental changes for abundant subcommunities. The results shed light on biogeography patterns and structuring mechanisms of bacterial communities in thermokarst lakes, improving our ability to predict the influences of future climate change on these lakes.

Abundant and rare soil fungi exhibit distinct succession patterns in the forefield of Dongkemadi glacier on the central Qinghai-Tibet Plateau

Glaciers are retreating rapidly, exposing extensive new soil habitats in glacier forefields and providing unique areas for studying primary succession. However, understanding the variation patterns and assembly mechanisms of abundant and rare fungi subcommunities along the glacier-retreating chronosequence remains a knowledge gap, especially true for the vast Qinghai-Tibet Plateau (QTP). Here, we investigated fungal communities in the glacier forefield in Dongkemadi Glaicer on the central QTP. The results showed that fungal alpha diversity exhibited a clear increasing pattern in response to increasing of distance to glacier. The percentage of abundant OTUs decreased while the percentage of rare OTUs increased, suggesting that soil development is more beneficial to the rare taxa. The distributions of both abundant and rare subcommunities exhibited a clear spatial pattern along the distance to glacier, and might be strongly controlled by multiple environmental variables, including pH, soil moisture, vegetation status, soil organic carbon, total nitrogen, and soluble reactive phosphorus. Abundant and rare fungal subcommunities were structured in different assembly regimes. Dispersal limitation processes were dominant for both abundant and rare subcommunities but with a stronger contribution to abundant subcommunity assembly. Heterogeneous selection processes contributed higher and non-dominant processes contributed lower to abundant subcommunities than to rare subcommunities. The modular structure of the fungal co-occurrence network was highly localized along the soil chronosequence. By revealing distinct diversity patterns and community assembly mechanisms of abundant and rare fungal subcommunities, our study improved our understanding of ecological succession along the glacier-retreating chronosequence.

Microeukaryotic Community Shifting Along a Lentic-Lotic Continuum

As an important regulator of ecosystem functions in river systems, microeukaryotes play an important role in energy and material conversion, yet little is known about the shift along a lentic-lotic continuum. In this study, the 18S rRNA genes sequencing was used to identify the microeukaryotic communities at 82 sites along a lentic-lotic continuum with the aim of understanding the impact of upstream inlet river on microeukaryotic communities in Baiyang Lake (BYD) and its downstream. Our results showed that the upstream inlet river affected the diversity and community composition of microeukaryotes in BYD and downstream rivers, and environmental variables greatly affected the composition of microeukaryotic community. The community composition in BYD had lower variabilities. Co-occurrence network analysis revealed that the network was non-random and clearly parsed into three modules, and different modules were relatively more abundant to a particular area. As keystone taxa, some nodes of the upstream microeukaryotic network played an important role in structuring network and maintaining the stability of the ecosystem. In BYD and downstream, the microeukaryotic network was highly fragmented, and the loss of keystone taxa would have an adverse impact on the integrity and function of the microeukaryotic community. Microeukaryotes had strong tendencies to co-occur, which may contribute to the stability and resilience of microeukaryotic communities. Overall, these findings extend the current understanding of the diversity and community composition of microeukaryotic along a lentic-lotic continuum.

Short-Term Grazing Exclusion Alters Soil Bacterial Co-occurrence Patterns Rather Than Community Diversity or Composition in Temperate Grasslands

Grazing exclusion is one of the most common practices for degraded grassland restoration worldwide. Soil microorganisms are critical components in soil and play important roles in maintaining grassland ecosystem functions. However, the changes of soil bacterial community characteristics during grazing exclusion for different types of grassland remain unclear. In this study, the soil bacterial community diversity and composition as well as the co-occurrence patterns were investigated and compared between grazing exclusion (4 years) and the paired adjacent grazing sites for three types of temperate grasslands (desert steppe, typical steppe, and meadow steppe) in the Hulunbuir grassland of Inner Mongolia. Our results showed that short-term grazing exclusion decreased the complexity and connectivity of bacterial co-occurrence patterns while increasing the network modules in three types of temperate grasslands. The effects of grazing exclusion on soil bacterial α-diversity and composition were not significant in typical steppe and meadow steppe. However, short-term grazing exclusion significantly altered the community composition in desert steppe, indicating that the soil bacteria communities in desert steppe could respond faster than those in other two types of steppes. In addition, the composition of bacterial community is predominantly affected by soil chemical properties, such as soil total carbon and pH, instead of spatial distance. These results indicated that short-term grazing exclusion altered the soil bacterial co-occurrence patterns rather than community diversity or composition in three types of temperate grasslands. Moreover, our study suggested that soil bacterial co-occurrence patterns were more sensitive to grazing exclusion, and the restoration of soil bacterial community might need a long term (>4 years) in our study area.

Abundant and Rare Bacterial Taxa Structuring Differently in Sediment and Water in Thermokarst Lakes in the Yellow River Source Area, Qinghai-Tibet Plateau

Thermokarst lakes are forming from permafrost thaw and are severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remains largely unknown, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided into abundant and rare according to their relative abundance, and the Sorensen dissimilarity (β_sor) was partitioned into turnover (β_turn) and nestedness (β_nest). The whole bacterial communities and the abundant and rare subcommunities differed substantially between sediment and water in taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. In general, bacterial communities are predominantly governed by strong turnover processes (β_turn/β_sor ratio of 0.925). Bacterial communities in sediment had a significantly higher β_turn/β_sor ratio than in water. Abundant subcommunities were significantly lower in the β_turn/β_sor ratio compared with rare subcommunities. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by heterogeneity in the source material, environmental filtering, and geographical isolation, leading to compositionally distinct communities. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapidly changing and vulnerable ecosystems.

Genomic Features and Molecular Function of a Novel Stress-Tolerant Bacillus halotolerans Strain Isolated from an Extreme Environment

Simple Summary

The Qinghai–Tibet Plateau is known as the “third pole of the world”. Due to the extreme geographical location, Qinghai–Tibet Plateau has unique ecosystems characterized by oxygen deficiency, low temperature, high salinity and alkalinity. We carried out the current study to explore the excellent extremophilic Bacillus strains via potential stress resistance as well as biocontrol properties in the Qinghai–Tibet Plateau. We found a Bacillus halotolerans strain with a promising ability to withstand harsh environments and which also exhibits an optimistic biocontrol activity against plant pathogens. We revealed the whole genome sequencing and its taxonomic position and elucidated its molecular functions that were responsible for enhancing stress tolerance as well as suppressing plant pathogens at the genetic level. Lastly, we identified this strain harbored the specific genes associated with stresses resistance, biocontrol function, and can be used as a biological agent in the agriculture field.

Abstract

Due to its topographical position and climatic conditions, the Qinghai–Tibet Plateau possesses abundant microorganism resources. The extremophilic strain KKD1 isolated from Hoh Xil possesses strong stress tolerance, enabling it to propagate under high salinity (13%) and alkalinity (pH 10.0) conditions. In addition, KKD1 exhibits promising biocontrol activity against plant pathogens. To further explore these traits at the genomic level, we performed whole-genome sequencing and analysis. The taxonomic identification according to the average nucleotide identity based on BLAST revealed that KKD1 belongs to Bacillus halotolerans. Genetic screening of KKD1 revealed that its stress resistance mechanism depends on osmotic equilibrium, membrane transportation, and the regulation of ion balance under salt and alkaline stress. The expression of genes involved in these pathways was analyzed using real-time quantitative PCR. The presence of different gene clusters encoding antimicrobial secondary metabolites indicated the various pathways by which KKD1 suppresses phytopathogenic growth. Moreover, the lipopeptides surfactin and fengycin were identified as being significant antifungal components of KKD1. Through comparative genomics analysis, we noticed that KKD1 harbored specific genes involved in stress resistance and biocontrol, thus providing a new perspective on the genomic features of the extremophilic Bacillus species.