Effects of variation in precipitation on the distribution of soil bacterial diversity in the primitive Korean pine and broadleaved forests

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Responses of soil bacterial communities to precipitation change in the semi-arid alpine grassland of Northern Tibet

A change in precipitation can profoundly change the structure of soil microbial communities, especially in arid and semi-arid areas which are limited by moisture conditions. Therefore, it is crucial to explore how soil bacterial community composition and diversity will respond to variation in precipitation. Here we conducted a precipitation control experiment to simulate precipitation change by reducing and increasing rainfall by 25%, 50%, and 75% in the alpine grasslands of northern Tibet. The composition, diversity, and species interaction network of soil microbial community were studied by high-throughput sequencing, and the relationship between microbial community species and soil environmental factors was analyzed. Our results showed that Proteobacteria (45%-52%) and Actinobacteria (37%-45%) were the dominant bacteria in the soil. The alpha diversity index based on Shannon, Chao1, and Simpson indices revealed that precipitation change had no significant effect on richness and evenness of soil microbial communities. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) showed that a clear separation of soil microbial communities between D2(-50%),D3(-75%) and W2(+50%), W3(+75%) treatments. The microbial interaction network indicated that the water-increasing treatment group had closer connections, and Proteobacteria and Actinomycetes were the core species. Furthermore, there was a stronger positive correlation between species in the water-reducing treatment group, the contribution of Proteobacteria decreased significantly, the role of connecting hub decreased, and Actinomycetes became the most important core microbial species. In addition, soil water content (SWC) and available phosphorus (AP) were closely related to the variations in soil microbial compositions. The findings of this study provide a theoretical basis for the driving mechanism of global climate change on soil microbial community and grassland ecosystem in alpine grassland.

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe

Currently, the impact of changes in precipitation and increased nitrogen(N) deposition on ecosystems has become a global problem. In this study, we conducted a 8-year field experiment to evaluate the effects of interaction between N deposition and precipitation change on soil bacterial communities in a desert steppe using high-throughput sequencing technology. The results revealed that soil bacterial communities were sensitive to precipitation addition but were highly tolerant to precipitation reduction. Reduced precipitation enhanced the competitive interactions of soil bacteria and made the ecological network more stable. Nitrogen addition weakened the effect of water addition in terms of soil bacterial diversity and community stability, and did not have an interactive influence. Moreover, decreased precipitation and increased N deposition did not have a superimposed effect on soil bacterial communities in the desert steppe. Soil pH, moisture content, and NH₄⁺-N and total carbon were significantly related to the structure of bacterial communities in the desert steppe. Based on network analysis and relative abundance, we identified Actinobacteria, Proteobacteria, Acidobacteria and Cyanobacteria members as the most important keystone bacteria that responded to precipitation changes and N deposition in the soil of the desert steppe. In summary, we comprehensively analyzed the responses of the soil bacterial community to precipitation changes and N deposition in a desert steppe, which provides a model for studying the effects of ecological factors on bacterial communities worldwide.

Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community

Paddy-upland rotation is an effective agricultural management practice for alleviating soil sickness. However, the effect of varying degrees of flooding on the soil microbial community and crop performance remains unclear. We conducted a pot experiment to determine the effects of two soil water content (SWC) and two flooding durations on the soil microbial community attributes and yield in cucumber. In the pot experiment, cucumber was rotated with cress single (45 days) or double (90 days) under 100 or 80% SWC. Then, the soil microbial were inoculated into sterilized soil to verified the relationship between cucumber growth and microorganisms. The results indicated single cress rotation resulted in a higher cucumber yield than double cress rotation and control. Cress rotation under 80% SWC had higher soil microbial diversity than cress rotation under 100% SWC and control. Flooding duration and SWC led to differences in the structure of soil microbial communities. Under 80% SWC, single cress rotation increased the relative abundance of potentially beneficial microorganisms, including Roseiflexus and Pseudallescheria spp., in cucumber rhizosphere. Under 100% SWC, single cress rotation increased the relative abundance of potentially beneficial bacteria, such as Haliangium spp., and decreased potential pathogenic fungi, such as Fusarium and Monographella spp., compared with double cress rotation and control. Varying degrees of flooding were causing the difference in diversity, structure and composition of soil microbial communities in the cucumber rhizosphere, which have a positive effect on cucumber growth and development.

Soil physicochemical properties drive the variation in soil microbial communities along a forest successional series in a degraded wetland in northeastern China

The Sanjiang Plain is the biggest freshwater wetland locating in northeastern China. Due to climate change and human activities, that wetland has degraded to a successional gradient from the original flooded wetland to dry shrub vegetation and a forest area with lower ground water level, which may result in changes in soil microbiologic structure and functions. The present study investigated the microbial diversity and community structure in relation to soil properties along that successional gradient. The soil physico-chemical properties changed significantly with degradation stage. The Shannon diversity index of both soil bacteria (5.90-6.42) and fungi (1.7-4.19) varied significantly with successional stage (both p < .05). The community structures of soil bacteria and fungi in the early successional stages (i.e., the wetland) were significantly determined by water content, total nitrogen, and available nitrogen concentrations in soils, while those in the later successional stages (i.e., forests) were significantly structured by soil organic carbon, soil pH, and available phosphorus concentrations. These results suggest that the soil microbial structure is mainly determined by soil properties rather than by plant community such as plant species composition along successional stages.

Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China

Variation in precipitation can markedly affect the structure and function of soil microbial communities, especially in arid areas which are limited by water resources. Therefore, it is critical to understand how soil bacterial community composition and diversity will respond to variation in precipitation. In this study, we examined the soil bacterial community structure and diversity between five precipitation treatments (60% decrease, 30% decrease, control, 30% increase and 60% increase in precipitation) in the same arid site, in the Junggar desert of Xinjiang, northern China. The dominant bacterial phyla, present at similar frequencies in plots with different precipitation levels, were Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. The Shannon-Wiener and Chao1 indices of soil bacterial α-diversity were both positively correlated with plant diversity. Our results indicated that (1) extreme drought significantly decreased bacterial abundance and diversity compared with increased precipitation; (2) variation in precipitation did not change the dominant components of the bacterial communities; and (3) soil pH and total nitrogen concentration were the key factors affecting soil bacterial composition in the Junggar desert.

Short-term response of the soil bacterial community to differing wildfire severity in Pinus tabulaeformis stands

In recent years, the investigation of fire disturbance of microbial communities has gained growing attention. However, how the bacterial community varies in response to different severities of fire at different soil depths is largely unknown. We utilized Illumina MiSeq sequencing to illustrate the changing patterns of the soil bacterial community following low-, moderate- and high-severity wildfire in the topsoil (0–10 cm) and subsoil (10–20 cm), 6 months after the fire. Acidobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia and Chloroflexi were the dominant phyla among all samples. Bacterial alpha diversity (i.e. Shannon and Simpson indices) in the topsoil was significantly higher than that in the subsoil after a high-severity wildfire. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) revealed significant differences in the bacterial community structure between the two soil layers. Soil pH, ammonium nitrogen (NH₄⁺-N) and total nitrogen were the main factors in shaping the bacterial community structure, of which soil pH was the most robust in both soil layers. Our study reveals that wildfire results in short-term changes in soil bacterial community. However, a long-term monitoring of microbial variation after burning is also essential.

Biogeographical distribution of bacterial communities in Changbai Mountain, Northeast China

The broad-leaved and Korean pine mixed forest in Changbai Mountain, China is an important component of boreal forest; the area is sensitive to global climate change. To understand spatial distribution patterns of soil bacterial community along elevation, we analyzed the soil bacterial community diversity and composition along an elevational gradient of 699-1177 m in a primitive Korean pine forest in Changbai Mountain using the high-throughput sequencing. In total, 149,519 optimized sequences were obtained. Bacterial Shannon index increased along elevation from 699 m to 937 m and started to decrease at the elevation of 1,044 m, showing a humpback curve along elevation. Evenness (ACE index) and richness (Chao index) of the soil bacterial community both decreased with elevation (the highest values of 770 and 762 at 699 m and the lowest values of 548 and 539 at 1,177 m, respectively), all the indices are significantly different between elevations. Bacterial composition at phylum and genus levels had some differences between elevations, but the dominant bacterial populations were generally consistent. Beta-diversity analysis showed a distance-decay pattern of bacterial community similarity at different samples. Soil physical and chemical properties explained 70.78% of the variation in bacterial community structure (soil pH explained 19.95%), and elevational distance only explained 8.42%. In conclusion, the contemporary environmental disturbances are the critical factors in maintaining the bacterial spatial distribution compared with historical contingencies.

Vertical zonation of soil fungal community structure in a Korean pine forest on Changbai Mountain, China

Changbai Mountain, with intact montane vertical vegetation belts, is located at a sensitive area of global climate change and a central distribution area of Korean pine forest. Broad-leaved Korean pine mixed forest (Pinus koraiensis as an edificator) is the most representative zonal climax vegetation in the humid region of northeastern China; their vertical zonation is the most intact and representative on Changbai Mountain. In this study, we analyzed the composition and diversity of soil fungal communities in the Korean pine forest on Changbai Mountain at elevations ranging from 699 to 1177 m using Illumina High-throughput sequencing. We obtained a total 186,663 optimized sequences, with an average length of 268.81 bp. We found soil fungal diversity index was decreased with increasing elevation from 699 to 937 m and began to rise after reaching 1044 m; the richness and evenness indices were decreased with an increase in elevation. Soil fungal compositions at the phylum, class and genus levels varied significantly at different elevations, but with the same dominant fungi. Beta-diversity analysis indicated that the similarity of fungal communities decreased with an increased vertical distance between the sample plots, showing a distance-decay relationship. Variation partition analysis showed that geographic distance (mainly elevation gradient) only explained 20.53 % of the total variation of fungal community structure, while soil physicochemical factors explained 69.78 %.