Distribution Of Soil Microbes Research Articles

Continental-scale insights into the soil microbial co-occurrence networks of Australia and their environmental drivers

Soil microbial communities and their interactions play a critical role in shaping the functions of ecosystems at regional and continental scales. In recent years, co-occurrence network analyses have provided a way to investigate microbial interactions among different microorganisms. But understanding how different environmental factors shape these networks at the continental scale remains challenging. Analyzing fungal, bacterial, and archaeal data from 166 study sites across Australia, we inferred a meta-community level soil microbial co-occurrence network for the Australian continent. Additionally, we analyzed node-level and network-level topological shifts associated with the five major vegetation types. Our results indicate that soils in the Australian savannah systems harbor a unique microbial association pattern, with the highest proportion of positive linkages, highest modularity and lowest average path length in comparison to soils from other vegetation types. Multi-model approaches revealed that different environmental drivers, including soil properties, temperature, and vegetation type, regulated the spatial distribution of topological parameters of the soil microbial networks analyzed in our study. We further generated high-resolution predication maps of microbial networks for Australia, providing insight into the distribution of soil microbes across the continent. By determining how the microbial co-occurrence networks vary according to vegetation type and mapping the distribution of the key parameters of these networks across Australia, we provide a unique understanding of microbial biogeography at the continental scale.

Distribution of Soil Microbes in Urban Parks: An Effect of Under-Tree Crown and Hillside Position on Testate Amoeba Assemblages in Subtropics (Shenzhen, China)

Testate amoebae (TA) are important components of soil ecosystems, where they play an essential role in belowground food webs. In this study, we examined species composition, diversity, and structure of TA assemblages in soils beneath tree crowns (microscale) at three slope positions (mesoscale) in subtropical urban parks in Shenzhen, China. Forty-two species of TA belonging to 18 genera were identified in 81 samples. TA assemblages were the most diverse and abundant in the center of the tree crown comparing with other under-tree habitats. Foot of the hills harbored higher TA abundance and diversity comparing with upper locations along the hillslopes. The distribution of TA was mostly driven by under-crown and hillside positions but not by elementary environmental conditions such as pH, moisture content and thickness of leaf litter layer. None of later factors were sufficient in shaping TA assemblage composition. The findings of our study suggest that in regional studies of soil microbial eukaryotes both micro- (i.e., under-crown) and mesoscale (i.e., the slope position) heterogeneity should be considered.

Distribution of soil microbes in urban parks: an effect of under-tree crown and hillside position on testate amoeba assemblages in subtropics (Shenzhen, China)

Distribution of soil microbes in urban parks: an effect of under-tree crown and hillside position on testate amoeba assemblages in subtropics (Shenzhen, China)

Soil fungal communities show more specificity than bacteria for plant species composition in a temperate forest in China

BackgroundSoil microbiome is an important part of the forest ecosystem and participates in forest ecological restoration and reconstruction. Niche differentiation with respect to resources is a prominent hypothesis to account for the maintenance of species diversity in forest ecosystems. Resource-based niche differentiation has driven ecological specialization. Plants influence soil microbial diversity and distribution by affecting the soil environment. However, with the change in plant population type, whether the distribution of soil microbes is random or follows an ecologically specialized manner remains to be further studied. We characterized the soil microbiome (bacteria and fungi) in different plant populations to assess the effects of phytophysiognomy on the distribution patterns of soil microbial communities in a temperate forest in China.ResultsOur results showed that the distribution of most soil microbes in different types of plant populations is not random but specialized in these temperate forests. The distribution patterns of bacteria and fungi were related to the composition of plant communities. Fungal species (32%) showed higher specialization than bacterial species (15%) for different types of plant populations. Light was the main driving factor of the fungal community, and soil physicochemical factors were the main driving factor of the bacterial community.ConclusionThese findings suggest that ecological specialization is important in maintaining local diversity in soil microbial communities in this forest. Fungi are more specialized than bacteria in the face of changes in plant population types. Changes in plant community composition could have important effects on soil microbial communities by potentially influencing the stability and stress resistance of forest ecosystems.

Humus microhabitat affects distributions of soil fungi and bacteria in a temperate mountain forest

AbstractHumus layer has an important effect on the diversity and spatial distribution of microbes. However, the role of partitioning of humus layer microhabitats for soil microbial diversity has been poorly documented. In this study, 120 soil samples were collected from a 5‐ha forest dynamic monitoring sample plot in a deciduous broad‐leaved forest. Clustering analysis was used to delineate microhabitats by humus layer. We explored diversity and community composition of soil fungi and bacteria using Illumina sequencing of the ITS rRNA gene and 16S rRNA gene region on the MiSeq platform. We investigated the diversity, species composition, and the microhabitat preferences of fungi and bacteria and then analyzed the effects of environmental factors on soil fungi and bacteria. Our results showed that the diversity, species composition, and the indicator species of the fungal and bacterial community varied among different humus layer microhabitats. In network analysis, the specialization indexes showed that 16.20%/22.30% of the fungal/bacterial operational taxonomic units (OTUs) had the characteristics of distribution specialization for humus layer microhabitats. Mantel test showed that the main environmental drivers of fungi and bacteria were not consistent among the four microhabitats. Our findings indicated that the distribution of soil microbes among humus layer microhabitats is not random, but specialized. We furthermore found that there were differences in the relationship between soil microbes and environment among microhabitats defined by humus layer. Together, these findings suggest the importance of partitioning of humus layer microhabitats in maintaining local diversity in a soil microbial community.

Physiochemical properties and microbial community characteristics of rhizosphere soil in Parashorea chinensis plantation

We explored the impacts of different mixed trees on the improvement of soil microecological environment in rhizosphere of Parashorea chinensis, including pure P. chinensis plantation (WC), mixed P. chinensis and Dalbergia odorifera plantation (WJ), mixed P. chinensis and Eucalyptus urophylla × E. grandis plantation (WA). Soil physical and chemical properties were analyzed. The characteristics and distribution of soil microbes in the rhizosphere were measured by the methods of Biolog-Eco micro plate and phospholipid fatty acid methyl ester (PLFA). Soil water content, soil pH, organic matter, total nitrogen, total potassium content and the activities of sucrase, urease and acid phosphatase in rhizosphere soil of WA were significantly higher than those of WC and WJ, without difference between WC and WJ. There were no significant differences in the contents of nitrate nitrogen, ammonium nitrogen, and available potassium between WA and WJ, which were obviously higher than those in WC. There were significant differences in total phosphorus and available phosphorus contents among the three stands, with an order of WJ>WA>WC. The average color change rate (AWCD), Shannon index, Simpson index, McIntosh index and the utilization of six types of carbon source substrates in microorganisms were the highest in the rhizosphere soil of WA, followed by WJ and WC. Results of principal component analysis showed that carbohydrates, amino acids and phenolic acids were the main carbon sources for microbial utilization. In WA, the PLFA content of rhizosphere soil microorganism, bacteria, fungi and actinomycetes was the highest, followed by WJ and WC. There were significant positive correlation between soil physical and che-mical properties and the microbial characteristics. Combining the physical and chemical properties of soil and the functional and structural characteristics of microbial communities, the mixed P. chinensis and E. urophylla × E.grandis plantation may be most conductive to the improvement of the rhizosphere microecological environment and increase soil available nutrients at the young tree phase of P. chinensis.

Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China.

Vegetation restoration is an available way to ameliorate degraded lands. In order to study the response of soil microbes to vegetation restoration in coal mining subsidence areas, the composition and distribution of soil microbes were discussed through three plots: unsubsided area (CA), new subsided area (NSA), and old subsided area (OSA) with different vegetation restoration time in Huabei coal mine. Meanwhile, changes in soil catalase and urease activity were explored and the correlation between soil bacteria, fungi, and environmental factors was analysed. The results demonstrated that Nitrospira was the dominant bacteria in all areas sampled. Microorganisms in the 0–20 cm and 40–60 cm soil layers of OSA had the highest Simpson index, whereas the index in NSA was lowest (at all soil depths). The catalase activity in NSA was significantly higher than that in CA, and there was no significant difference in catalase activity with soil depth, while the urease activity declined gradually with increasing soil depth. The urease activity in the 20–60 cm soil layer of NSA and OSA was significantly higher than that of CA. Furthermore, the distribution of bacteria was mainly affected by soil organic matter, available potassium, available phosphorus, and alkali-hydrolyzable nitrogen, whereas pH and catalase activity mainly affected fungal distribution. These results implied that soil catalase activity in NSA and urease activity in the 20–40 cm soil layer of NSA and OSA were significantly enhanced after vegetation restoration, and that long-term plant restoration could improve soil fertility and soil microbial community diversity in coal mining areas.

Investigations of relationships among aggregate pore structure, microbial biomass, and soil organic carbon in a Mollisol using combined non-destructive measurements and phospholipid fatty acid analysis

Limitations of traditional measurement methods have impeded progress in understanding the role of soil aggregation in protecting soil organic carbon (SOC) from decomposition by soil microbes living in pore spaces. In this paper, we used the Scanning Electronic Microscope (SEM) and X-ray micro Computed Tomography (micro-CT) to study the relationships of the aggregate pore structure and microbial distribution in the interior and exterior of soil aggregates, and thereby gained an insight into protection of carbon within macroaggregates of an undisturbed Mollisol in northeastern China. There were close relationships between soil pore structure and distribution of soil microbes and soil organic carbon (SOC), but they were different on the exterior and interior of soil aggregate. On the exterior of macroaggregates, there were negative relationships between soil porosities, the number of pores and SOC, especially for soil pores in the 10–30 μm and 30–100 μm classes, indicating these two pore sizes are unlikely to help sequester C. In contrast, there was a positive correlation between soil pores > 100 μm and SOC. Furthermore, soil pore structure had no impact on soil microbial biomass and density or on SOC contents in the interior of soil aggregates. This study provides a new method by combining SEM with micro-CT technology for linking soil structure and soil microbial properties with C sequestration and SOC changes.

Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert.

The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal–Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus–Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.

Responses of peat carbon at different depths to simulated warming and oxidizing

Warming and water table drawdown greatly reshape peatland carbon cycle, especially when considering the old carbon stored under the peatland subsurface. However, little is known about the effects of warming, oxidizing by drying or their combination on carbon decomposition at different depths (0–100 cm) of peat. In this research, soil of different depths from Zoige Plateau was incubated in four scenarios (8 °C-anaerobic, 8 °C-aerobic, 18 °C-anaerobic and 18 °C-aerobic) to detect the exported carbon. Our result showed that soil respiration (Rs) increased obviously with enhanced temperature and oxygen. The total CO2 fluxes of 2400.22 ± 57.69 mg m-2 d-1 under 8 °C-anaerobic condition increased by 73.6%, 40.7% and 176.5% with warming, oxidizing and their combined effect, respectively. The average dissolved organic carbon (DOC) concentration was 74.90 ± 8.09 mg kg-1 under 8 °C-anaerobic condition, but increased by 53.5%, 44% and 159.4%, respectively under the condition of warming, oxidizing and their combination. Rs and its variation under warming and oxidization differed significantly among different depths, probably caused by the differences of soil substrate, especially the variation in distribution of soil microbes and enzymes among depths of peatlands. By classifying the source of Rs as young soil (YS: 0–20 cm) and old soil (OS: 21–100 cm), this reseaerch found that OS accounted for a huge part of total Rs under 8 °C-anaerobic condition (CO2: 74.2%; DOC: 60.7%). Such relative contribution of OS to total Rs did not change obviously with warming or oxidizing. Though YS and OS responded equally to warming and oxidizing, OS was responsible for a larger proportion of total increase in Rs. Compared with other studies, we concluded that peatlands soil in our field of mid-latitude and high altitude is less sensitive to warming and oxidizing than peatlands of higher latitude, but that OS of this peatlands is more critical in predicting regional carbon cycle.

荒漠灌木梭梭（Haloxylon ammodendron）土壤微生物的空间分布

荒漠灌木梭梭（<i>Haloxylon ammodendron</i>）土壤微生物的空间分布