Distribution Of Soil Microbial Communities Research Articles

Changes in Nutrient-Regulated Soil Microbial Communities in Soils Concomitant with Grassland Restoration in the Alpine Mining Region of the Qilian Mountains

In response to the significant ecological damage caused by unsustainable mining practices in the Qilian Mountains, ecological restoration projects have been undertaken in recent years. Analyzing the changes in soil microbial communities during the restoration process of mine meadows helps to reveal the mechanism of the restoration process in alpine mining areas. To explore the characteristics of soil microbial community distribution and their relationships with soil environmental factors during the restoration of alpine grasslands in the Qilian Mountains, we conducted surveys and analyses in two restoration levels low restoration (LR) and high restoration (HR) in the eastern Qilian Mountains, along with an undisturbed natural grassland control (NG). We found that as the degree of high-altitude mining area recovery increases, there were significant increases in vegetation cover, vegetation height, above-ground biomass, vegetation Shannon–Wiener index, soil organic carbon (SOC), soil water content (SWC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available phosphorus (AP), and available nitrogen (AN). Conversely, soil pH and electrical conductivity (EC) significantly decreased, with soil pH decreasing from 6.93 to 4.13. Restoration of high-altitude mining area grasslands significantly alters the distribution and composition of soil bacteria and fungi, while the impact on soil microbial community changes was not significant. Notably, with increasing recovery level, the dominant bacterial phyla are Acidobacteria and Proteobacteria, while the dominant fungal phyla are Ascomycota and Basidiomycota. These results indicate that changes in vegetation and soil properties both affect the composition of soil microbial communities, with soil properties having a greater influence. Soil fertility and nutrient levels emerge as the primary drivers influencing soil microbial composition communities and the degree of high-altitude mining area grassland recovery.

Combined Application Effects of Arbuscular Mycorrhizal Fungi and Biochar on the Rhizosphere Fungal Community of Allium fistulosum L.

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

Soil microbes support Janzen's mountain passes hypothesis: The role of local-scale climate variability along a tropical montane gradient.

Tropical montane ecosystems are the centers of biodiversity, and Janzen proposed that mountain climate variability plays a key role in sustaining this biodiversity. We test this hypothesis for soil bacteria and fungi along a 265-1,400 m elevational gradient on Hainan Island of tropical China, representing diverse vegetation types from deciduous monsoon forest to cloud forest. We found that bacterial and fungal diversity declined as elevation increased, and the dissimilarity of both groups increased with increasing separation in elevation, although changes in bacteria were larger than in fungi. Seasonal alterations and the range of soil moisture in the growing season were found to be the dominant drivers of fungal richness and Shannon diversity, whereas soil pH was the major driver of bacterial diversity. Dissimilarities of bacterial and fungal communities were best predicted by climate, particularly seasonal changes in soil temperature, with weaker influences of soil physicochemistry and vegetation. The dominant effect of seasonality in soil temperature was further detected in cloud forests, which harbored a higher proportion of unique bacterial species and dissimilarity of bacterial and fungal communities. Our findings suggest that local-climate variability plays a crucial role in structuring the distribution of soil microbial communities along a tropical montane gradient, which generally supports Janzen's hypothesis. Such a sensitivity to climatic variability suggests that soil microbial communities along tropical montane gradients may shift in response to future climate scenarios.

A review on influence of biochar amendment on soil processes and environmental remediation

ABSTRACT Biochar is the thermal degradation product of biomass generated in an oxygen-limited environment under different pyrolysis conditions. Biochar characteristics are functions of the feedstock material and pyrolysis temperature. Depending on pyrolysis conditions biochar concentrates varying quantities of recalcitrant and labile carbon along with nutrients which in turn affect soil physiochemical properties and microbial processes. Biochar in soil balances carbon content encourages nitrogen fixation and solubilize phosphorus along with enhancing soil enzyme activity. It serves as a microhabitat for microorganisms present in soil thus influences the diversity, composition, and distribution of soil microbial communities by affecting their intra- and interspecific communication. This review provides an overview of the current knowledge about biochar characteristics, its interactions with soil, and associated biota and its role in soil remediation. In addition, this paper also discussed the factors affecting the capacity of biochar to adsorb organic pollutants following different mechanisms. Being an effective adsorbent due its high specific surface area, large porosity, and numerous surface functional groups biochar has been explored extensively in field of environment to remediate contaminated soils.

Space Rather than Seasonal Changes Explained More of the Spatiotemporal Variation of Tropical Soil Microbial Communities.

Soil microbiomes play an essential role in maintaining soil geochemical cycle and function. Although there have been some reports on the diversity patterns and drivers of the tropical forest soil microbial community, how space and seasonal changes affect spatiotemporal distribution at the regional scales are poorly understood. Based on 260 soil samples, we investigated the spatiotemporal patterns of rubber plantations and rainforest soil microbial communities across the whole of Hainan Island, China during the dry and rainy seasons. We examined soil bacterial and fungal composition and diversity and the main drivers of these microbes using Illumina sequencing and assembly. Our results revealed that the diversity (both alpha and beta) spatiotemporal variation in microbial communities is highly dependent on regional location rather than seasonal changes. For example, the site explained 28.5% and 37.2% of the variation in alpha diversity for soil bacteria and fungi, respectively, and explained 34.6% of the bacterial variance and 14.3% of the fungal variance in beta diversity. Soil pH, mean annual temperature, and mean annual precipitation were the most important factors associated with the distribution of soil microbial communities. Furthermore, we identified that variations in edaphic (e.g., soil pH) and climatic factors (e.g., mean annual temperature [MAT] and mean annual precipitation [MAP]) were mainly caused by regional sites (P < 0.001). Collectively, our work provides empirical evidence that space, rather than seasonal changes, explained more of the spatiotemporal variation of soil microbial communities in tropical forests, mediated by regional location-induced changes in climatic factors and edaphic properties. IMPORTANCE The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). Moreover, the environmental factors were mainly explained by geographic location effect rather than by seasonal effect, and environmental dissimilarity significantly increased with geographic distance. In conclusion, our study provides solid empirical evidence that space rather than season explained more of the spatiotemporal variation of soil microbial communities in the tropical forest.

Warming alters elevation distributions of soil bacterial and fungal communities in alpine grasslands

It is still unknown whether climate warming can change the elevation distribution of soil microbial communities in alpine grasslands. Both species and phylogenetic β-diversity of soil bacterial and fungal communities were investigated at three alpine grasslands (site A: 4300 m, site B: 4500 m, and site C: 4700 m) after 7–8 years of experimental warming. Three main findings were observed. First, warming may increase species β-diversity of soil bacterial community between altitudes, while decrease species β-diversity of soil fungal community between altitudes. This finding may be due to their (species β-diversity of soil bacterial community vs. fungal community) different relationships with environmental factors and different responses of ecological processes in determining the community turnover between elevations to warming. Second, compared to phylogenetic β-diversity, species β-diversity of soil bacterial and fungal communities between elevations had diverse responses to warming. This finding may be related to species and phylogenetic β-diversity had different correlations with environment variables (e.g., soil moisture had the greatest contribution to soil bacterial species β-diversity between elevations, but the ratio of available nitrogen to phosphorus had the greatest contribution to soil bacterial phylogenetic β-diversity between elevations under warming scenes). Third, warming effects on species and phylogenetic β-diversity of soil bacterial and fungal communities between elevations varied with years (e.g., for soil fungal community, the phylogenetic β-diversity between elevation 4300 m and 4500 m was reduced after 7-year of experimental warming, but increased after 8-year of experimental warming), which may be due to interannual variability in climate conditions, relative contributions of ecological processes in determining the community turnover between elevations, and warming effects on the differences of soil variables between elevations. In summary, warming can reconstruct the elevation distribution patterns of soil bacterial and fungal communities, and the reconstruction can vary with β-diversity type (i.e., phylogenetic versus species β-diversity) and year.

Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands.

Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

BackgroundSoil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.ResultsBacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.ConclusionsThis study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.

VNIR and MIR spectroscopy of PLFA-derived soil microbial properties and associated soil physicochemical characteristics in an experimental plant diversity gradient

Improving our understanding of the functions and processes of soil microbial communities and their interactions with the physicochemical soil environment requires large amounts of timely and cost-efficient soil data, which is difficult to obtain with routine laboratory-analytical methods. Soil spectroscopy with portable visible-to-near infrared (VNIR) and mid-infrared (MIR) instruments can fill this gap by facilitating the rapid acquisition of biotic and abiotic soil information.In this study, we evaluated the capabilities of VNIR and MIR spectroscopy to analyze soil physicochemical and microbial properties in a long-term grassland biodiversity-ecosystem functioning experiment. Soil samples were collected at the Jena Experiment (Jena, Germany) and measured with portable VNIR and MIR spectrometers in field-moist condition to determine their potential for on-site data collection and analysis. Reference data to calibrate spectroscopic models were acquired with routine analytical methods, including PLFA extractions of microbial biomarkers. We further collected reference VNIR and MIR data on pre-treated soils (dried and finely ground) to assess the anticipated impact of field measurements on spectroscopic calibrations.MIR spectra allowed more accurate estimates of soil physicochemical and microbial properties than VNIR data on pre-treated samples. For soils in field condition, MIR calibrations were more accurate for physicochemical properties, but VNIR data gave significantly better estimates of microbial properties. Combined VNIR/MIR estimates achieved the most accurate estimation results for all soil properties in each case.Soil physicochemical properties could be estimated from VNIR/MIR data with high accuracy (R2 = 0.72–0.99) on pre-treated soil samples, whereas the results for soil microbial properties were more moderate (R2 = 0.66–0.72). On field-moist soils, estimation accuracies decreased notably for organic and inorganic carbon (ΔRMSE = 52–72%), improved slightly for soil texture (ΔRMSE = 4–7%) and decreased slightly for microbial properties (ΔRMSE = 4–9%). The VNIR/MIR estimates derived from soils in field condition were sufficiently accurate to detect experimental plant treatment effects on organic carbon, as well as bacterial and fungal biomass. We further found that spectroscopic estimates of soil microbial properties were primarily enabled through indirect correlations with spectrally active soil constituents, i.e., associations between soil microbial properties and the physicochemical soil environment.Our findings highlight the capacity of VNIR and MIR spectroscopy to analyze the physicochemical soil environment, including potential on-site data collection and analysis on soils in field condition, and indicate that VNIR/MIR data can estimate soil microbial properties when soil physicochemical properties shape the distribution of soil microbial communities.

Soil bacterial community composition and functional potentials along the vertical vegetation transect on Mount Segrila, Tibet, China

Information on the spatial distribution of soil microbial communities on the Tibetan Pla-teau is critical for in-depth understanding the important roles of microbes in typical alpine ecosystems. In this study, 16S rDNA Illumina Miseq sequencing was used to analyze the variations in bacterial community composition and functional potentials in soils sampled from four elevations on Mount Segrila, Tibet, and the driving environmental factors. Results showed that richness and Shannon diversity index of soil bacteria significantly decreased with increasing altitude. The relative abundances of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Nitrospirae significantly increased, whereas that of Proteobacteria, Actinobacteria and Bacteroidetes significantly decreased with increasing altitude. In KEGG pathway (level Ⅱ), the relative abundance of genes related to membrane transport and the metabolism of amino acids, lipids, terpenoids and polyketones was significantly lower at high elevations. In contrast, genes related to carbohydrates metabolism, signal transduction, replication and repair and enzyme family were more abundant at high altitudes. Soil bacterial community composition and predicted functions were significantly affected by vegetation types and soil properties, with soil pH being the key driver. There were significant correlations between the abundances of predicted functions and bacterial taxa, such as Acitnobacteria, Bacteroidetes, and Fibrobacteres. The dissimilarity in the composition of KEGG pathway genes along the elevational gradient (β-diversity) showed a significantly positive correlation with the dissimilarity in bacterial community structure, indicating that there was a strong relationship between microbial community composition and potential functionality.

Soil microbial community responses to long-term nitrogen addition at different soil depths in a typical steppe

Global nitrogen (N) deposition has been influencing the structure of soil microbial communities, which play fundamental roles in modifying most biogeochemical processes. However, to date, our understanding of how long-term N deposition affects soil microbial communities, particularly those in subsurface soil, is largely incomplete. In this study, we examined soil microbial phospholipid fatty acids at different depths in the soil profile, including in topsoil (0–10 cm), midsoil (30–40 cm), and subsoil (70–100 cm), in a 10-year N addition experimental site in a semiarid steppe. We collected soil samples at four N addition treatment levels, including 0, 2, 10, and 50 g m−2 year−1, which represented control, low-N, medium-N, and high-N inputs, respectively. Our results showed that N addition remarkably shifted soil microbial communities by increasing the relative abundances of bacteria and Gram-positive (GP) bacteria, and decreasing Gram-negative (GN) bacterial relative abundance across the three soil layers by affecting soil pH and NO3−-N, particularly under the medium- and high-N addition rates. Moreover, the effects of N addition tended to increase with the N addition rate but diminished with soil depth. Soil pH, NO3−-N, and NH4+-N were the most important driving factors for changes in microbial community composition in topsoil, whereas soil total N (TN) and total carbon were important in midsoil, and TN, dissolved organic N, and soil moisture were important in subsoil. The relative abundances of bacteria and GN bacteria also decreased, whereas those of fungi and GP bacteria increased with soil depth regardless of N addition. Soil TN and pH were the most important factors in shaping the vertical distribution of soil microbial communities. Our results suggest that both N addition and soil depth may cause similar microbial community shifts, through which fungi and GP bacteria become dominant, but through different mechanisms. These results suggest that it is important to distinguish among the N-deposition effects on soil microbial communities at different soil depths when building soil system models.

Long-term nitrogen fertilization alters microbial community structure and denitrifier abundance in the deep vadose zone

The excessive use of nitrogen (N) fertilizer in intensive agriculture has increased nitrate leaching into groundwater, but its impacts on N transformation processes and the associated microbial communities in the deep vadose zone remain unclear. Soil samples from 0–1050 cm depth were collected from a 20-year field experiment with two N fertilization treatments: 0 (N0) and 600 kg N ha−1 year−1 (N600). Amplicon sequencing and quantitative PCR analyses were performed to profile the vertical distribution of soil microbial communities and denitrification genes. The soil microbial community structure and diversity were strongly influenced by soil depth and N fertilization. The 250 cm depth was identified as a threshold depth, as dramatically different microbial communities were found below and above this depth. Quantitative PCR results showed that the absolute abundance of denitrification genes decreased with increasing soil depth. This study elucidated the profound effects of long-term N input on the composition and diversity of the microbial communities and the abundance of denitrifiers in the deep vadose zone. Our results provide basic information for use in mitigating nitrate leaching by enhancing microbial denitrification in deep vadose zones in intensive agricultural areas.

Distinct assembly processes shape bacterial communities along unsaturated, groundwater fluctuated, and saturated zones

The subsurface soil environment through the unsaturated (vadose) zone and saturated (below groundwater table) zone is one of the most active layers in the Earth's surface with biogeochemical interactions. Geochemical variables and geographic distance are key driving forces shaping the distribution of soil microbial communities, but our understandings are mainly limited to surface soil or shallow unsaturated zone (1–3 m beneath the ground). In this study, soil and sediment samples were collected from the unsaturated zone, through groundwater fluctuated zone, to saturated zone (up to 20 m) to unravel the assembly processes mediating vertical bacterial community succession across these three zones. Our results suggested both geochemical niches and bacterial diversity had different vertical patterns in each zone. With increased depth, pH increased and nutrient levels (C, N, P, K) and bacterial diversity declined in the unsaturated zone, and nutrients and bacterial diversity remained low levels after reaching the fluctuated and saturated zones. Nutrients were the key drivers shaping bacterial variation in the unsaturated zone, but limited nutrients and only ‘depth’ significantly explained the variations in the fluctuated zone and saturated zone, respectively. The co-occurrence network supported a more species co-existence pattern in the unsaturated zone than that in the other two zones. Due to the geochemical variations across three zones, the assembly of phylogenetically more clustered communities was observed through deterministic processes (e.g., 55% homogenizing selection) in the unsaturated zone, but the stochastic process (e.g., 50%–70% dispersal limitation) was more important in the fluctuated and saturated zones. These findings together suggested that the vertical distribution of soil bacterial community assembly was zone-specific and shaped by the degree of deterministic vs. stochastic processes. Our results provide a novel insight into the microbial community assembly across three different ecosystems in the Earth's critical zone and shed a light on subsurface biogeochemical processes.

Dynamic changes in microbial communities and nutrient stoichiometry associated with soil aggregate structure in restored wetlands

Available information on interaction mechanisms between soil nutrient stoichiometry and microbial communities associated with soil aggregate structure in restored wetlands remains limited. As such, this study investigated water-stable aggregate structure using wet-sieving method and scanning electron microscope (SEM) in restored wetlands with a restoration duration of 0, 1, 2, 3, 5, 13 or 19 years, and their internal nutrient stoichiometry and microbial communities (phospholipid fatty acid analysis, PLFAs). The results showed that soil aggregate structure tended to be stable from the fifth restoration year. In the restored wetlands, General bacteria, Gram-positive bacteria (G+), and Gram-negative bacteria (G−) were the dominant components of soil microorganisms, which tented to condense in coarse-aggregates. The carbon-to-phosphorus (C:P) and nitrogen-to-phosphorus (N:P) ratios were higher in coarse-aggregates since C and N benefit from the physical protection. Redundancy analysis (RDA) results indicated that C:N ratio was primary environmental factors controlling the distribution of soil microbial communities. In the Sanjiang Plain, the soil organic carbon (SOC) decomposition was lower, and N was the primary nutrient limiting wetland restoration quality.

Soil bacterial community structures across biomes in artificial ecosystems

Soil microorganisms are important for maintaining multiple functions of terrestrial ecosystems. Understanding the spatial and temporal distribution of soil microbial communities and their key determinants is one of the central goals of microbial ecology. In this study, we used an artificial ecosystem called the Ecorium, which a system with a series of biomes including tropical forest, desert, Mediterranean grassland and temperate forest. By using an artificial ecosystem, it is possible to understand the distribution of microbial communities and their key determinants under the control for potential confounds such as soil chronosequence, pedogenesis, ecosystem development stages and historical processes. Two years after construction of the Ecorium, we analyzed bacterial community structures using Illumina Miseq as well as measuring the chemical properties of the soil samples. The relationship between bacterial communities and soil chemical properties was then analyzed. Across all of the biomes, the most abundant phylum was Proteobacteria (36.0 ± 3.0%), followed by Actinobacteria (14.6 ± 3.1%), Bacteroidetes (12.4 ± 0.4%) and Acidobacteria (11.7 ± 3.2%). Bacterial alpha diversity was highest in the temperate biome and lowest in the control soil and desert biome. Bacterial community structure differed significantly between the control soil and that of the rest of the biomes, as well as among the biomes themselves. We found that the impact of climate factors was larger than that of biotic factors, such as vegetation diversity, in the structuring of bacterial communities. Soil water content appeared to be the most influential factor in determining microbial community structure. The results of this study provide a better understanding of the relationship and interaction between soil microbial ecology and environmental factors on a wide geographical scale. This information could be applied to technologies for ecosystem restoration, as well as the establishment of sustainable ecosystem management strategies and conservation policies.

Response of organic carbon fractions and microbial community composition of soil aggregates to long-term fertilizations in an intensive greenhouse system

PURPOSE: Soil organic carbon (SOC) content and stability, which are regulated by microbial communities, vary depending on aggregate size. The objectives of this study were to investigate the distribution of the SOC fraction and microbial community composition within soil aggregates when subjected to different fertilization treatments. MATERIALS AND METHODS: This study used high-throughput sequencing technology to analyze the soil microbial community distribution in different-sized aggregate fractions [> 2 mm (large macro-aggregates), 2–0.25 mm (small macro-aggregates), and < 0.25 mm (microaggregates)] when they were subjected to different fertilization treatments in a 16-year greenhouse experiment. The three treatments were chemical fertilizer (CF), 50% organic fertilizer + 50% chemical fertilizer (MF), and organic fertilizer (OF). RESULTS AND DISCUSSION: The results showed that the application of organic fertilizer significantly increased the soil organic carbon (SOC), dissolvable organic carbon (DOC), and microbial biomass carbon (MBC) contents and changed microbial community composition in all the different-sized soil aggregates. We observed that OF significantly reduced the relative abundance of bacterial communities in all aggregates and significantly increased the relative abundances of fungal communities in small macro-aggregates. The larger fungal communities in small macro-aggregates could promote soil aggregation and C sequestration. CONCLUSIONS: Organic fertilization increased the substrate contents in soil aggregates and enhanced soil aggregation and microbial activity in macro-aggregates, which are critical factors that facilitate C transformation and sequestration. These improvements resulted in significantly improved soil fertility and increased vegetable yield in the greenhouses.

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe.

We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.

Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities.

Tillage can strongly affect the long-term productivity of an agricultural system by altering the composition and spatial distribution of nutrients and microbial communities. The impact of tillage methods on the vertical distribution of soil microbial communities is not well understood, and the correlation between microbial communities and soil nutrients vertical distributions is also not clear. In the present study, we investigated the effects of conventional plowing tillage (CT: moldboard plowing), reduced tillage (RT: rotary tillage), and no tillage (NT) on the composition of bacterial and fungal communities within the soil profile (0–5, 5–10, 10–20, and 20–30 cm) using high-throughput sequencing of the microbial 16S/ITS gene. Microbial communities differed by soil properties and sampling depth. Tillage treatment strongly affected the microbial community structure and distribution by soil depth, and changed the vertical distribution of soil bacterial and fungal communities differently. Depth decay of bacterial communities was significantly smaller in CT than in RT and NT, and that of fungal communities were significantly greater in RT than CT and NT. The presence/absence of species was the main contributing factor for the vertical variation of bacterial communities, whereas for fungal communities the main factor was the difference in relative abundance of the species, suggesting niche-based process was more important for bacterial than fungal community in structuring the vertical distribution. Soil total carbon was correlated more with soil bacterial (especially the anaerobic and facultatively anaerobic groups) than with fungal community. These results suggested different roles of bacteria and fungi in carbon sequestration of crop residue and in shaping soil carbon distribution, which might impact on soil fertility.

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

BackgroundThe relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau.ResultsOur results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%.ConclusionsOur findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.