scholarly journals Towards a function-first framework to make soil microbial ecology predictive

2021 ◽  
Author(s):  
Johannes Rousk ◽  
Lettice Hicks
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Functional Response ◽  
Community Composition ◽  
Ecosystem Function ◽  
Bacterial Growth ◽  
Response Curve ◽  
Ecosystem Functions ◽  
Soil Microbial

<p>Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions.</p><p>We first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial functions on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of “biomarker” taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition.</p><p>In this presentation, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.</p>

Viewing soil systems from the top-down can make microbial ecology predictive for ecosystem functions

2020 ◽  
Author(s):  
Johannes Rousk ◽  
Lettice Hicks
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Functional Response ◽  
Community Composition ◽  
Ecosystem Function ◽  
Response Curve ◽  
Ecosystem Processes ◽  
Ecosystem Functions ◽  
Top Down

<p>Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community structure.</p><p>Here, we propose a new conceptual framework to determine how microbial communities influence ecosystem processes, by applying a “top-down” approach. Looking from the “top”, we first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial community processes on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates), allowing us to define the aggregate functional response curve of the community. We then demonstrate that the whole community contribution to ecosystem function can be predicted, by parameterising the functional response curve with current environmental conditions. In a final step, we show how this functional information can be linked to the taxonomic community composition (amplicon assessments of microbial community composition) in order to identify “biomarker” taxa that capture microbial communities’ regulation of ecosystem processes and the susceptibility of microbial community structure and function to environmental change. Ultimately, these biomarkers may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition information combined with environmental metadata.</p>

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Effects of Microbial Consortia, Applied as Fertilizer Coating, on Soil and Rhizosphere Microbial Communities and Potato Yield

2021 ◽  
Vol 3 ◽  
Author(s):  
William Overbeek ◽  
Thomas Jeanne ◽  
Richard Hogue ◽  
Donald L. Smith
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Bulk Soil ◽  
Microbial Inoculants ◽  
Flowering Stage ◽  
Soil Microbial ◽  
Soil Microbial Community Composition

The use of biological inputs in crop production systems, as complements to synthetic inputs, is gaining popularity in the agricultural industry due to increasing consumer demand for more environmentally friendly agriculture. An approach to meeting this demand is the inoculation of field crops with beneficial microbes to promote plant growth and resistance to biotic and abiotic stresses. However, the scientific literature reports inconsistent results following applications of bio-inoculant to fields. The effects of inoculation with beneficial microbes on bulk soil and rhizospheric microbial communities is often overlooked as precise monitoring of soil microbial communities is difficult. The aim of this research was to use Illumina high throughput sequencing (HTS) to shed light on bulk soil and rhizospheric microbial community responses to two commercial microbial inoculants coated onto fertilizer granules, applied to potato fields. Bulk soil samples were collected 4 days before seeding (May 27th), 7 days after seeding (June 7th), at potato shoot emergence (June 21st) and at mid-flowering (July 26th). Rhizospheric soil was collected at the mid-flowering stage. The Illumina MiSeq HTS results indicated that the bulk soil microbial community composition, especially prokaryotes, changed significantly across potato growth stages. Microbial inoculation did not affect bulk soil or rhizospheric microbial communities sampled at the mid-flowering stage. However, a detailed analysis of the HTS results showed that bulk soil and rhizospheric microbial community richness and composition were different for the first treatment block compared to the other three blocks. The spatial heterogeneity of the soil microbial community between blocks of plots was associated with potato tuber yield changes, indicating links between crop productivity and soil microbial community composition. Understanding these links could help in production of high-quality microbial inoculants to promote potato productivity.

Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases

Plant Disease ◽  
2022 ◽  
Author(s):  
Yajiao Wang ◽  
Shuping Tian ◽  
Nan Wu ◽  
Wenwen Liu ◽  
Li Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Chemical Properties ◽  
Ecological Factors ◽  
Severity Index ◽  
Paddy Soils ◽  
Bacterial Diseases ◽  
Soil Microbial

Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.

scholarly journals Apple Root stocks and Pre-plant Soil Treatments Alter Soil Microbial Community Composition in a New York Orchard

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1128C-1128
Author(s):  
Shengrui Yao ◽  
Ian A. Merwin ◽  
Janice E. Thies
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Growth And Yield ◽  
Soil Microbial ◽  
Plant Soil ◽  
Soil Microbial Community Composition

Apple (Malu ×domestica) replant disease (ARD) is a soil-borne disease syndrome of complex etiology that occurs worldwide when establishing new orchards in old fruit-growing sites. Methyl bromide (MB) has been an effective soil fumigant to control ARD, but safer alternatives to MB are needed. We evaluated soil microbial communities, tree growth, and fruit yield for three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and five clonal rootstocks (M7, M26, CG6210, CG30, and G16), in an apple replant site at Ithaca, N.Y. Molecular fingerprinting (PCR-DGGE) techniques were used to study soil microbial community composition of root-zone soil of the different soil treatments and rootstocks. Tree caliper, shoot growth, and yield were measured annually from 2002–04. Among the five rootstocks we compared, trees on CG6210 had the most growth and yield, while trees on M26 had the least growth and yield. Soil treatments altered soil microbial communities during the year after pre-plant treatments, and each treatment was associated with distinct microbial groups in hierarchical cluster analyses. However, those differences among fungal and bacterial communities diminished during the second year after planting, and soil fungal communities equilibrated faster than bacterial communities. Pre-plant soil treatments altered bulk-soil microbial community composition, but those shifts in soil microbial communities had no obvious correlation with tree performance. Rootstock genotypes were the dominant factor in tree performance after 3 years of observations, and different rootstocks were associated with characteristic bacterial, pseudomonad, fungal, and oomycetes communities in root-zone soil.

Effects of simulated drought and warming on microbial responses to drying and rewetting in contrasting land-uses

2020 ◽  
Author(s):  
Ainara Leizeaga ◽  
Lettice C. Hicks ◽  
Albert C. Brangarí ◽  
Menale Wondie ◽  
Hans Sandén ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Growth ◽  
Forest Soils ◽  
Fungal Growth ◽  
Land Uses ◽  
Soil Microbial ◽  
Drying And Rewetting ◽  
Microbial Responses ◽  
Simulated Drought

<p>Climate change will increase temperatures and the frequency and intensity of extreme drought and rainfall events. When a drought period is followed by a rainfall event, there is a big CO<sub>2</sub> pulse from soil to the atmosphere which is regulated by soil microorganisms. In the present study, we set out to investigate how simulated drought and warming affects the soil microbial responses to drying and rewetting (DRW), and how those responses will interact with the level of land degradation. Previous work has shown that exposure DRW cycles in the laboratory and in the field can induce changes in the microbial community such that it resumes growth rates faster after a DRW cycle. In addition, it has been observed that a history of drought in both a humid heathland ecosystem in Northern Europe and in semi-arid grasslands in Texas can select for microorganisms with a higher carbon use efficiency (CUE) during DRW. In this study we tested if these observations could be extended to subtropical environments.</p><p>Rain shelters and open top chambers (OTC) were installed in Northwestern Ethiopia in two contrasting land-uses; a degraded cropland and a pristine forest. Soils were sampled (>1-year field treatments) and exposed to a DRW cycle in the laboratory. Microbial growth and respiration responses were followed with high temporal resolution over 3 weeks. We hypothesized that (i) simulated drought would result in more resilient and efficient microbial communities to DRW, while (ii) simulated warming should leave microbial community traits linked to moisture unchanged. In addition, (iii) we hypothesized that microbial communities would recover growth rates faster in the cropland since that ecosystem is more prone to DRW events.</p><p>Microbial responses in both land-uses and treatments universally showed a highly resilient type of community response with both bacterial growth and fungal growth increasing immediately upon rewetting, linked with the expected respiration pulse. The field treatments simulating drought and warming did not affect the already high resilience of soil microbial communities to DRW cycles. However, differences between the rates of recovery between fungi and bacteria were observed. Fungal growth recovered faster than bacterial growth, peaking c. 15 h in comparison to bacteria that peaked at c.20h after rewetting. Simulated drought reduced the microbial CUE during rewetting in croplands without affecting the forest soils. The CUE was also elevated in the warming treatments in both land-uses, and generally higher in croplands than in forest soils. Taken together, the responses in microbial CUE during the rewetting of dry soils were likely linked to either (i) differences in resource availability which were higher in warming treatments and in croplands compared to forests, or (ii) selection of  more efficient microbial communities due to a higher exposure to DRW events driven by the higher temperatures in the cropland, and increased evapotranspiration in the warming treatments.</p><div> <div> <div> </div> </div> </div>

scholarly journals Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area

2020 ◽  
Vol 17 (16) ◽  
pp. 5680
Author(s):  
Xingqing Zhao ◽  
Jian Huang ◽  
Xuyan Zhu ◽  
Jinchun Chai ◽  
Xiaoli Ji
Keyword(s):  
Heavy Metal ◽  
Community Structure ◽  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Metal Pollution ◽  
Heavy Metal Pollution ◽  
Mining Area ◽  
Soil Microbial

The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun’an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun’an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (PN). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.

scholarly journals Soil Bacterial and Fungal Response to Wildfires in the Canadian Boreal Forest Across a Burn Severity Gradient

2019 ◽  
Author(s):  
Thea Whitman ◽  
Ellen Whitman ◽  
Jamie Woolet ◽  
Mike D Flannigan ◽  
Dan K Thompson ◽  
...  
Keyword(s):  
Boreal Forest ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Microbial Communities ◽  
Total Carbon ◽  
Burn Severity ◽  
Ecosystem Functions ◽  
Moisture Regime ◽  
Soil Microbial ◽  
Canadian Boreal Forest

Global fire regimes are changing, with increases in wildfire frequency and severity expected for many North American forests over the next 100 years. Fires can result in dramatic changes to C stocks and can restructure plant and microbial communities, which can have long-lasting effects on ecosystem functions. We investigated wildfire effects on soil microbial communities (bacteria and fungi) in an extreme fire season in the northwestern Canadian boreal forest, using field surveys, remote sensing, and high-throughput amplicon sequencing. We found that fire occurrence, along with vegetation community, moisture regime, pH, total carbon, and soil texture are all significant predictors of soil microbial community composition. Communities become increasingly dissimilar with increasingly severe burns, and the burn severity index (an index of the fractional area of consumed organic soils and exposed mineral soils) best predicted total bacterial community composition, while burned/unburned was the best predictor for fungi. Globally abundant taxa were identified as significant positive fire responders, including the bacteria Massilia sp. (64x more abundant with fire) and Arthrobacter sp. (35x), and the fungi Penicillium sp. (22x) and Fusicladium sp. (12x) Bacterial and fungal co-occurrence network modules were characterized by fire responsiveness as well as pH and moisture regime. Building on the efforts of previous studies, our results identify specific fire-responsive microbial taxa and suggest that accounting for burn severity improves our understanding of their response to fires, with potentially important implications for ecosystem functions.

scholarly journals Deintensification of land use leads to recovery of soil microbial community composition and function after land use change in Ethiopia

2021 ◽  
Author(s):  
Yoseph Delelegn ◽  
Witoon Purahong ◽  
Ali Nawaz ◽  
Hans Sandén ◽  
Douglas Godbold ◽  
...  
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Land Use Change ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Ecosystem Functions ◽  
Soil Microbial

Ethiopia has undergone significant land use change during the past centuries, particularly deforestation. These changes have resulted in the loss of topsoil as well as the associated soil ecosystem functions. Grazing exclusion and planting of eucalyptus are measures used to recover degraded lands and reduce deforestation, respectively. Using a gradient of the intensity of land use from natural forest to croplands, we investigated whether these measures also result in restoration of the soil microbial community. We identified the soil bacterial and fungal communities using paired-end amplicon sequencing. A total of 12,765 fungal and 12,325 bacterial OTUs were detected in the five land use types, and only ca. 2% and 17% were shared among the land uses, respectively. Total fungal and bacterial OTU richness was not significantly affected by land use change, but the conversion of forest to cropland resulted in the loss of approximately 40% and 11% of the total native fungal and bacterial OTUs, respectively. Soil pH, C, N, and aggregate stability were key factors corresponding to the overall bacterial and fungal community compositions. We also showed relationships between the microbial functional group and enzyme activities. The exclusion of grazing led to an enrichment of soil microbial communities that overlapped with the communities of the natural forest. Our results suggest that remnant native forests act as refugia for microbial communities and that restoration of microbial communities and concomitant recovery of ecosystem function via deintensification of land use is possible. Keywords: ectomycorrhiza, ericoid mycorrhiza, exclosure, microbial diversity, soil enzymes

Sign in / Sign up

Export Citation Format

Share Document