Distribution Of Soil Bacterial Communities Research Articles

The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity.

To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland's restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities' structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.

Distribution pattern and influencing factors of bacterial communities in different soil depths of Caragana jubata shurb in Luya Mountain, China.

Soil microorganisms are important components of terrestrial ecosystems, affecting soil formation and fertility, plant growth and stress tolerance, nutrient turnover and carbon storage. In this study, we collected soil samples (humus layer, 0-10 cm, 10-20 cm, 20-40 cm, and 40-80 cm) from Caragana jubata shrubland in Shanxi subalpine to explore the composition, diversity, and assembly of soil bacterial communities at different depths across the soil profile. The results showed that Actinomycota (19%-28%), Chloromycota (10%-36%) and Acidobacteria (15%-24%), and Proteobacteria (9%-25%) were the dominant bacterial phyla. α-diversity of soil bacterial community significantly decreased with the increases of soil depth. Soil bacterial β-diversity varied across different soil depths. Soil pH, water content, and enzyme activity were the main ecological factors affecting the distribution of soil bacterial communities. Soil bacterial communities had more complex interactions in humus layer and 0-10 cm layer. On the whole, soil bacterial communities were dominated by coexistence in C. jubata shrubland, and the soil bacterial community assembly was driven by random process.

Soil pH controls the structure and diversity of bacterial communities along elevational gradients on Huangshan, China

Acquiring knowledge of the patterns of soil microbial diversity along elevational gradients and the driving factors of these patterns is important for understanding the dynamics of global nutrient elements. In this study, we analyzed the soil bacterial community composition and diversity using Illumina high-throughput sequencing along an elevational gradient from 670 to 1780 m on Huangshan including 6 vegetation types from base to summit. We found that the dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi, accounting for more than 75 % of the sequences. We observed significant variation in soil bacterial community composition across different elevations (ANOSIM P = 0.001). In addition, the soil bacterial diversity increased with increasing elevation from 875 m to 1165 m and decreased with increasing elevation from 1280 m to 1370 m, showing a humpbacked relationship with elevations. Soil pH had the strongest effect on bacterial community composition. In conclusion, soil properties, especially soil pH was the primary factor controlling the elevational distribution of soil bacterial communities on Huangshan.

Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient.

Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.

Strong partitioning of soil bacterial community composition and co-occurrence networks along a small-scale elevational gradient on Zijin Mountain

The elevational distributions of bacterial communities in natural mountain forests, especially along large elevational gradients, have been studied for many years. However, the distributional patterns that underlie variations in soil bacterial communities along small-scale elevational gradients in urban ecosystems are not yet well understood. Using Illumina MiSeq DNA sequencing, we surveyed soil bacterial communities at three elevations on Zijin Mountain in Nanjing City: the hilltop (300 m a.s.l.), the hillside (150 m a.s.l.), and the foot of the hill (0 m a.s.l.). The results showed that edaphic properties differed significantly with elevation. Bacterial community composition, rather than alpha diversity, strongly differed among the three elevations (Adonis: R2 = 0.12, P<0.01). Adonis and DistLM analyses demonstrated that bacterial community composition was highly correlated with soil pH, elevation, total nitrogen (TN), and dissolved organic carbon (DOC). The degree scores, betweenness centralities, and composition of keystone species were distinct among the elevations. These results demonstrate strong elevational partitioning in the distributions of soil bacterial communities along the gradient on Zijin Mountain. Soil pH and elevation together drove the small-scale elevational distribution of soil bacterial communities. This study broadens our understanding of distribution patterns and biotic co-occurrence associations of soil bacterial communities from large elevational gradients to short elevational gradients.

Bacterial community changes and their responses to nitrogen addition among different alpine grassland types at the eastern edge of Qinghai–Tibetan Plateau

Soil microbes play a fundamental role in maintaining nutrient biogeochemical cycles. To understand the distribution of soil bacterial communities on grassland plateaus, high-throughput sequencing was used to compare bacterial communities in soils from swamp meadows (SM), alpine meadows (AM), alpine steppes (AS), and desert steppes (DS) at the eastern edge of the Qinghai-Tibetan Plateau (QTP) in China. We then compared response to nitrogen addition between SM and DS soils in microcosms. Bacterial α-diversity decreased from SM > AM > AS > DS. Variations in soil properties across grassland types was associated with different soil bacterial communities corresponding to bacterial species associated with nutrient cycles to those associated with degradation. Soil moisture, pH, and total phosphorus were the main drivers of these differences. Nitrogen addition decreased bacterial diversity but had inconsistent effects on soil bacterial communities in SM and DS, which may also indicate that different alpine grassland soil types have unique bacterial communities. Alpine grassland degradation significantly affects bacterial communities, and the response to nitrogen addition depends on the alpine grassland type. These results allow for better predictions of soil bacteria community-level responses to geochemical and environmental change in alpine areas.

Soil acidification modifies soil depth-microbiome relationships in a no-till wheat cropping system

Soil pH is among the most important drivers of soil bacterial community composition and diversity. However, most studies exploring the spatial distribution of soil bacterial communities have focused on the top 10–20 cm of soil, leaving our knowledge of the composition, diversity, and forces structuring subsoil communities relatively unexplored. Moreover, in agricultural soil managed without tillage (no-till), fertilizers often generate an acidified soil layer in the seed zone, rendering no-till soils a unique system in which to study the relative impacts of pH and soil depth on microbial communities. We characterize the composition and diversity of bacterial communities in a no-till wheat-based cropping system from eastern Washington, across soil depths (0 cm, 10 cm, 25 cm, 50 cm, 75 cm, and 100 cm). Soil depth was a strong driver of bacterial community composition and diversity. Proteobacteria and Actinobacteria dominated the soil surface, Acidobacteria peaked in relative abundance at 10 cm, and Actinobacteria and unidentified taxa were greatest in relative abundance below 25 cm. However, acidified soil disrupted relationships between soil depth and bacterial communities, resulting in a low diversity and distinct composition of bacterial communities at the 10 cm depth. Co-occurrence networks of bacterial taxa revealed groups of co-occurring taxa that responded primarily to soil pH or depth. This work provides an insight on the distribution and drivers of bacterial communities in deep soil profiles in dryland wheat-based cropping systems.

Soil bacterial community structure of mixed bamboo and broad-leaved forest based on tree crown width ratio

Moso bamboo (Phyllostachysheterocycla (Carr.) Mitford cv. Pubescens) is an economically valuable plant in bamboo production areas of southern China, for which the management mode is crucial for improving the comprehensive benefits of bamboo forest stands. In this respect, mixed forested areas of bamboo and broad-leaved tree species can provide sound ecological management of bamboo in forestry operations. To further this goal, an outstanding question is to better understand the spatial distribution of soil bacterial communities in relation to the proportion of mixed in bamboo and broad-leaved forest. We analyzed soil bacterial community diversity and composition along a proportional gradient of 0–40% mixed-ratio (as represented by the width and size of the broad-leaved tree crown over the plot area) of bamboo and broad-leaved forest in Tianbao Yan Nature Reserve using the highthroughputsequencing of the 16S rRNA gene.Specifically, the sampling plots for the mixed proportions were divided according to the percentage of summed projected area of live broadleaf tree crowns. The main broad-leaved species in the five mixed ratio plots are the same. Each plot was 20 m × 20 m in size, and a total of 15 plots were established, three per forest ratio class. From each plot, soil samples were taken at the surface (0–10 cm depth) in December 2017. Our analysis revealed that soil bacterial diversity community structure and dominant flora changed under different mixing ratios of bamboo and broad-leaved trees. In the stand with a mixed ratio of 10–20%, the bacterial diversity index is higher; however, the diversity was lowest in the 20–30% stands. Among the 20–30% forest soil, Acidobacteria (Solibacteria, Solibacteriales, Acidobacteriales) was more abundant than in soils from other mixed-ratio stands.Redundancy analysis showed that mixed forest stand structure, soil pH, organic carbon, total nitrogen, and soil moisture all contributed to shaping the bacterial community structure. Changes in microbial communities were associated with species diversity in tree layers, availability of soil nutrients (SOC and TN), and changes in soil physical properties (MS, pH). Together, these empirical results suggest that different mixing ratios in the bamboo–broad-leaved mixed forest could influence the soil bacterial community structure indirectly, specifically by affecting the soil physical and chemical properties of the forest.

Habitat-specific environmental factors regulate spatial variability of soil bacterial communities in biocrusts across northern China's drylands

Biocrusts are common biotic components in dryland ecosystems worldwide, they contain diverse soil organisms and effectively enhance soil stability and perform a series of key ecological functions. However, the geographical pattern of microbial communities in biocrusts is rarely assessed, despite it is closely related to the spatial variation of ecosystem functions in drylands. We assessed soil bacterial communities in biocrusts across four ecosystems (Gobi, desert, desert steppe and grassland) in a precipitation gradient (16–566 mm yr−1) in northern China. Bacterial OTU number and phylogenetic diversity did not linearly increase with decreasing aridity, they were significantly lower in Gobi and similar among desert, desert steppe and grassland. Soil bacterial community composition in Gobi and desert were different than those in desert steppe and grassland, and they were similar between Gobi and desert, this suggests the key role of habitat in structuring soil bacterial communities. The geographic pattern of soil bacterial communities was strongly influenced by both geographic distance and environmental factors. The first explanatory factor for the geographic variation of bacterial community dissimilarity differed among four ecosystems, being aridity in Gobi and desert, precipitation in desert steppe, and soil inorganic nitrogen in grassland. The geographic pattern of the bacterial functional group profile showed a similar pattern with community composition across four ecosystems, and the groups of containing mobile elements and gram negative bacteria were more abundant in drier habitats of Gobi and desert. Our results reveal the non-linear changes in diversity, composition and functional group of soil bacterial communities in biocrusts across the precipitation gradient from hyper-arid to semi-humid regions, and suggest that the geographic distance and habitat-specific environmental factors determine the distribution of soil bacterial communities in different ecosystems.

Vertical changes in bacterial community composition down to a depth of 20 m on the degraded Loess Plateau in China

AbstractSoil microbes are involved in the fundamental processes that underpin an ecosystem's function. However, little is known about the microbial communities that inhabit deep soil horizons, especially in degraded forest ecosystems. Here, we used high‐throughput sequencing to investigate the vertical distribution of soil bacterial communities to a depth of 20 m in Pinus tabulaeformis and Robinia pseudoacacia forests on the Loess Plateau, China. We found that bacterial richness declined from the topsoil to a depth of 2 m in P. tabulaeformis forests and declined from the topsoil to a depth of 1 m in R. pseudoacacia forests, and thereafter increased. The relative abundance of α‐Proteobacteria was higher in subsoils than in topsoils of P. tabulaeformis forests. It was highest at the depth of 20 or 14 m in both forest types, suggesting that α‐Proteobacteria can survive dry, alkaline, low‐nutrient environments. We also found a higher relative abundance of Acidobacteria in topsoils than in subsoils, indicating that Acidobacteria can grow well in nutrient‐rich environments. Our results suggest that soil bacterial communities respond to nutrient changes associated with soil depth and plant species. These findings revealed that soil microorganisms persisted in deep and carbon‐starved soils, especially for α‐Proteobacteria, which may be adapted to resource‐poor environments in deep soils.

Local-scale variation of soil bacterial communities in ice-free regions of maritime Antarctica

The majority of biogeographic studies in Antarctic terrestrial ecosystems have focused on macroscopic eukaryote taxa. In contrast, microbial taxa have been almost neglected or examined without sufficient spatial coverage. Here, we examined the spatial distribution of soil bacterial communities and their relation to local environmental gradients in ice-free regions of the maritime Antarctic. Soils in this region were dominated by Actinobacteria and Proteobacteria, which are typically found in Antarctic soils. Notably, candidate divisions AD3 and WPS-2, which rarely occur in other biomes, were found in high abundance in acidic surface soils. Soil pH and total organic carbon (TOC) were the primary drivers of the bacterial community structure and various geochemical variables also played important roles in structuring bacterial community composition. Bacterial communities were significantly correlated to measured environmental variables, most of which are spatially structured at the local spatial scale (0.5–8 km). This suggests that spatial heterogeneity of environmental factors is an important driver of shifts in bacterial communities. Although various sets of environmental variables were related to bacterial communities, a large proportion of community variation remained unexplained. This indicates that bacterial communities in Antarctic soils may be governed by other biotic or abiotic factors which are not typically measured in other biome studies.

The Biogeographical Distribution of Soil Bacterial Communities in the Loess Plateau as Revealed by High-Throughput Sequencing

The rigorous environmental stress of the severely eroded Loess Plateau may have promoted specific soil bacterial communities in comparison to other eco-environmental regions. In order to unmask the bacterial diversity and most influential environmental parameters, Illumina MiSeq high throughput sequencing of 16S rRNA from 24 representative soil samples collected across south-east to north-west transect of the Loess Plateau in northern Shaanxi, China was conducted. This high-throughput sequencing revealed a total of 1,411,001 high quality sequences that classified into 38 phyla, 127 classes, >240 orders, and over 650 genera, suggesting a high bacterial richness across the Loess Plateau soils. The seven dominant groups were: Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, and Verrucomicrobi (relative abundance of >5%). Increasing/decreasing soil pH and geographic longitudinal distance correlated significantly with increasing/decreasing bacterial richness and diversity indices. Pairwise correlation analysis showed higher bacterial diversity at longitudinal gradients across 107°39′-109°15′ (south-east to north-west) in our studied Chinese loess zone. Variation partitioning analysis indicated significant influence of soil characteristics (~40.4%) than geographical distance (at a landscape scale of ~400 km) that was responsible for 13.6% of variation in bacterial community structure from these soils. Overall, contemporary soil characteristics structure the bacterial community in Loess Plateau soil to a greater extent than the spatial distances along the loess transect.

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil.

Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina’s MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve.

Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

The biogeography of soil archaeal communities on the eastern Tibetan Plateau.

The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = −0.47, P < 0.01). Spatial distance, a potential measure of the legacy effect of evolutionary and dispersal factors, was less important than measured environmental factors in determining the broad scale archaeal community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.