scholarly journals Microbiome of vineyard soils is shaped by geography and management

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Emanuela Coller ◽  
Alessandro Cestaro ◽  
Roberto Zanzotti ◽  
Daniela Bertoldi ◽  
Massimo Pindo ◽  
...  
Keyword(s):  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Its Sequencing ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Specific Effects ◽  
Bacteria And Fungi ◽  
Italian Province

Abstract Background Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management. Results Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil. Conclusions Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

scholarly journals Soil Fungal Communities Investigated by Metabarcoding within Simulated Forensic Burial Contexts

2020 ◽  
Author(s):  
Noemi Procopio ◽  
Stefano Ghignone ◽  
Samuele Voyron ◽  
Marco Chiapello ◽  
Anna Williams ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Experimental Studies ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Post Mortem ◽  
Morphological Examination ◽  
Soil Microbial ◽  
Fungal Biomarkers ◽  
Bacteria And Fungi ◽  
Pmi Estimation

Abstract Background One of the most debated questions in forensic science is the estimation of the post-mortem interval (PMI). Despite the large amount of research currently performed to improve the PMI estimation, there is still the need for additional improvements, particularly in cases of severely decomposed buried remains. A novel alternative to the morphological examination of the remains is the analysis of the soil microbial communities. Bacteria and fungi are ubiquitous and can be found in the soil and in/on the corpses, and their shifts in populational compositions present at different PMIs may reveal insights for PMI estimation. Despite it already having been revealed that bacteria might be good candidates for this type of analysis, there are knowledge gaps for this type of application when dealing with fungal communities. For this reason, we performed the metabarcoding analysis of the mycobiome present in the soil after prolonged decomposition times, from one- to six-months, targeting both the Internal Transcribed Spacer (ITS) 1 and 2, to elucidate which of the two was more suitable for this purpose. Results Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs and the presence of specific trends associated with specific PMIs, such as the increase of the Mortierellomycota taxa after four- and six-months post-mortem and of Ascomycota particularly after two months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited amount of taxa specifically associated with the presence of the mammalian carcasses and not present in the control soil, showing that the overall the taxa which are contributing the most to the changes in the community originate from the soil and are not introduced by the carrion, extending the potential to perform comparisons with other experimental studies with different carrion species. Conclusions This study has been the first one conducted on gravesoil, and sets the baseline for additional studies, showing the potential to use fungal biomarkers in combination with bacterial ones to improve the accuracy of the PMI predictive model based on the shifts in the soil microbial communities.

scholarly journals Long-Term Drought and Warming Alter Soil Bacterial and Fungal Communities in an Upland Heathland

Ecosystems ◽  
2021 ◽  
Author(s):  
Fiona M. Seaton ◽  
Sabine Reinsch ◽  
Tim Goodall ◽  
Nicola White ◽  
Davey L. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Its2 Region ◽  
Rrna Gene ◽  
Summer Drought ◽  
Soil Microbial ◽  
Soil Bacterial

AbstractThe response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site degradation

2019 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Biological Factor ◽  
Rrna Gene ◽  
Biological Factors ◽  
Soil Microbial ◽  
Relative Abundances ◽  
Bacteria And Fungi ◽  
Degree Of Degradation

Abstract Background: Jinsha earthen site in Chengdu, China, plays an important role in understanding the ancient culture and history of Shu civilization. The site is undergoing soil degradation due to physical, chemical and biological factors, while very little is known about the influence of biological factors on earthen sites. To investigate the biological factor, we analyzed microbial communities and physicochemical properties from samples with no obvious, mild, moderate and severe degradation, referred to as S1, S2, S3 and S4 sample groups, respectively.Results: Amplicon sequencing targeting the 16S rRNA gene and ITS for bacteria and fungi, respectively, revealed high bacterial and relatively low fungal diversity; the bacterial OTUs were assigned into 36 phyla and 617 genera and the fungal OTUs into 5 phyla and 205 genera. The relative abundances of Bacteroidetes, Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of degradation. In the genus level, the relative abundances of Bacteroides and Ralstonia were higher and that of Rubrobacter lower with higher degree of degradation. The distribution of the fungal genera in the four sample groups seemed more random than that of bacteria; however, the relative abundance of the yeast genus Candida was highest in the severely degraded sample group. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH 4 + , K + , Mg 2+ , Ca 2+ and SO 4 2- .Conclusion: Taken together, the microbial communities in soil with different degree of degradation were distinctly different at Jinsha earthen site, and degradation was accompanied with bigger changes in the bacterial than in the fungal community.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration

2020 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Yeast Genus ◽  
Soil Microbial ◽  
Physicochemical Factors ◽  
Permanent Loss ◽  
Relative Abundances ◽  
Bacteria And Fungi

Abstract Background: Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on the physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the communities and their correlation with environmental factors, and compare community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa.Results: The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. Conclusion: The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

scholarly journals Soil Microbial Communities Altered by Titanium Ions in Different Agroecosystems of Pitaya and Grape

2021 ◽  
Author(s):  
Yuan He ◽  
Xinrong Ma ◽  
Xin-Yi Hou ◽  
Cai-Xia Li ◽  
Yan Wang
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Foliar Spray ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Significant Difference

Abstract Titanium ions can significantly promote plant growth, but it is unclear whether the application of titanium ions to plants has any effect on the soil microbial community. In this study, we conducted field surveys to determine the effect of titanium ions on soil microbial communities of the pitaya and grape plantations in Panxi area by performing full-length 16S rRNA gene and ITS amplicon sequencing using PacBio Sequel. The results showed that the application of titanium ions significantly altered the composition and structure of soil microbiota. Root irrigation with titanium ions in pitaya garden, the diversity of soil fungi was significantly reduced. Although there was no statistically significant difference, bacterial diversity also declined. While, the foliar spray of titanium ions on grapes greatly reduced the soil microbial diversity. Moreover, the soil microbiota had a core of conserved taxa, and their relative abundances were significantly altered by titanium ions. Moreover, titanium ions enhanced the cooccurrence relationships and probably improved the stability of the soil microbial community. Our results highlight the different responses of bacterial and fungal communities to titanium ions and sites and provides a basis for the application of titanium ions in plant farming.

scholarly journals Soil Bacteria and Fungi Respond Differently to Organisms Covering on Leshan Giant Buddha Body

2021 ◽  
Vol 13 (7) ◽  
pp. 3897
Author(s):  
Xuli Chen ◽  
Manfei Wang ◽  
Fujia Wu ◽  
Bo Sun ◽  
Tianyu Yang ◽  
...  
Keyword(s):  
Vascular Plants ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Terrestrial Ecosystems ◽  
Diversity Indices ◽  
Scientific Basis ◽  
Soil Microbial ◽  
Α Diversity ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi

Soil microbial communities play a key role in the functioning of terrestrial ecosystems, in particular through their interaction with above-ground plants and weathering of rocks. In this study, the chemical properties and microbial diversity of soils covered by different organisms on Leshan Giant Buddha body were analyzed. The results showed that the concentration of soil total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) increased significantly with the change of above-ground organisms from lichens to bryophytes and vascular plants. TOC, TN, TP, C:N, and C:P were significantly correlated with the composition of microbial community. Bacterial and fungal diversity responded differently to the change of organisms, and the diversity of bacterial communities changed significantly among different sites. The settlement of Embryogenic plants increased the α-diversity indices including Sobs, Shannon, Ace and Chao indices, which were highest in sites covered with Ferns. The relative abundances of Chloroflexi, Acidobacteria, Nitrospirae and Planctomycetes increased with the order of Bryophyte, Fern, Grass and Shrub, and Cyanobacteria was opposite, with the highest in samples covered with lichens. These results improve understanding of plant–fungi–bacteria interactions during the early stages of soil development, and provide a scientific basis for protection of Leshan Giant Buddha.

scholarly journals Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Bin Ma ◽  
Zhongmin Dai ◽  
Haizhen Wang ◽  
Melissa Dsouza ◽  
Xingmei Liu ◽  
...  
Keyword(s):  
Eastern China ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Community Diversity ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Continental Scale ◽  
Forest Sites ◽  
Vegetation Gradient ◽  
Bacteria And Fungi

ABSTRACT Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

scholarly journals Associations between human impacts and forest soil microbial communities

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Yongjian Chen ◽  
Jialiang Kuang ◽  
Pandeng Wang ◽  
Wensheng Shu ◽  
Albert Barberán
Keyword(s):  
Microbial Communities ◽  
Forest Soil ◽  
Human Activity ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Nitrifying Bacteria ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Soil Microbial ◽  
Soil Variables

We are living in a new epoch—the Anthropocene, in which human activity is reshaping global biodiversity at an unprecedented rate. Increasing efforts are being made toward a better understanding of the associations between human activity and the geographic patterns in plant and animal communities. However, similar efforts are rarely applied to microbial communities. Here, we collected 472 forest soil samples across eastern China, and the bacterial and fungal communities in those samples were determined by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer region, respectively. By compiling human impact variables as well as climate and soil variables, our goal was to elucidate the association between microbial richness and human activity when climate and soil variables are taken into account. We found that soil microbial richness was associated with human activity. Specifically, human population density was positively associated with the richness of bacteria, nitrifying bacteria and fungal plant pathogens, but it was negatively associated with the richness of cellulolytic bacteria and ectomycorrhizal fungi. Together, these results suggest that the associations between geographic variations of soil microbial richness and human activity still persist when climate and soil variables are taken into account and that these associations vary among different microbial taxonomic and functional groups.

scholarly journals Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1526
Author(s):  
Xiaoqin Yang ◽  
Yang Wang ◽  
Luying Sun ◽  
Xiaoning Qi ◽  
Fengbin Song ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Northeast China ◽  
Management Practice ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Crop Productivity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

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