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 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 Animal soil food web complexity triggers shifts in microbial communities, including PAH degraders, but without clear effects on phenanthrene phytoremediation

2021 ◽  
Author(s):  
Sara Correa-García ◽  
Vincenzo Corelli ◽  
Julien Tremblay ◽  
Jessica Ann Dozois ◽  
Eugenie Mukula ◽  
...  
Keyword(s):  
Food Web ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Soil Food Web ◽  
Experimental Conditions ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Degradation Rates ◽  
Food Web Complexity

The aim of this study was to determine whether the complexity of the animal soil food web (SFWC) is a significant factor influencing the soil microbial communities, the productivity of the willow, and the degradation rates of 100 mg kg-1 phenanthrene contamination. The SFWC treatment had eight levels: just the microbial community (BF), or the BF with nematodes (N), springtails (C), earthworms (E), CE, CN, EN, CEN. After eight weeks of growth, the height and biomass of willows were significantly affected by the SFWC, whereas the amount of phenanthrene degraded was not affected, reaching over 95% in all pots. SFWC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFWC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many PAH degraders. These SFWC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to the Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFWC treatments. Overall, our results suggest that, under our experimental conditions, SFWC does not affect significantly willow phytoremediation outcomes.

scholarly journals Does a carbonatite deposit influence its surrounding ecosystem?

FACETS ◽  
2019 ◽  
Vol 4 (1) ◽  
pp. 389-406
Author(s):  
James M.C. Jones ◽  
Elizabeth A. Webb ◽  
Michael D.J. Lynch ◽  
Trevor C. Charles ◽  
Pedro M. Antunes ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Chemistry ◽  
Soil Microbial Communities ◽  
Soil Nutrient ◽  
Vegetation Survey ◽  
Northern Ontario ◽  
Soil Microbial ◽  
Bacteria And Fungi ◽  
First Time

Carbonatites are unusual alkaline rocks with diverse compositions. Although previous work has characterized the effects these rocks have on soils and plants, little is known about their impacts on local ecosystems. Using a deposit within the Great Lakes–St. Lawrence forest in northern Ontario, Canada, we investigated the effect of a carbonatite on soil chemistry and on the structure of plant and soil microbial communities. This was done using a vegetation survey conducted above and around the deposit, with corresponding soil samples collected for determining soil nutrient composition and for assessing microbial community structure using 16S/ITS Illumina Mi-Seq sequencing. In some soils above the deposit a soil chemical signature of the carbonatite was found, with the most important effect being an increase in soil pH compared with the non-deposit soils. Both plants and microorganisms responded to the altered soil chemistry: the plant communities present in carbonatite-impacted soils were dominated by ruderal species, and although differences in microbial communities across the surveyed areas were not obvious, the abundances of specific bacteria and fungi were reduced in response to the carbonatite. Overall, the deposit seems to have created microenvironments of relatively basic soil in an otherwise acidic forest soil. This study demonstrates for the first time how carbonatites can alter ecosystems in situ.

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 Arable agriculture changes soil microbial communities in the South African Grassland Biome

2018 ◽  
Vol 114 (5/6) ◽  
Author(s):  
Gilbert Kamgan Nkuekam ◽  
Don A. Cowan ◽  
Angel Valverde
Keyword(s):  
Microbial Communities ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
The Impact ◽  
Natural Grassland

Many studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition.

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.

Microbial temperature adaptation across a European gradient

2021 ◽  
Author(s):  
Carla Cruz Paredes ◽  
Daniel Tajmel ◽  
Johannes Rousk
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Growth ◽  
Microbial Community Composition ◽  
Thermal Adaptation ◽  
Soil Microbial Communities ◽  
Fungal Growth ◽  
Fungal Communities ◽  
Soil Microbial

<p>Temperature is one of the most important environmental factors controlling both microbial growth and respiration. Warmer temperatures accelerate the rate at which microorganisms respire. Therefore, it is expected that climate warming will induce losses of carbon to the atmosphere through soil microbial respiration, representing a positive feedback to climate warming. However, there are multiple gaps in our understanding on responses of microorganisms to warming. For instance, long-term experiments have shown that the increase in soil respiration found in warming experiments diminishes with time, recovering to ambient values. This suggests that soil C losses might not be as extensive as previously suggested. This can be due to substrate depletion or shifts in the microbial community composition that led to thermal adaptation. To test thermal adaptation of soil microbial communities to their climate, variation along latitudinal gradients is a useful context. Such geographical gradients have long-term and large temperature differences thus patterns in thermal adaptation should have had sufficient time for ecological and evolutionary processes to act, allowing us to test if soil microbial communities have adapted to thermal regimes.</p><p>We investigated a latitudinal gradient across Europe with 76 sites that spanned a gradient of decadal mean annual temperature (MAT) from -3.1 to 18.3°C. We investigated if respiration, bacterial and fungal growth responses were adapted to long-term temperature differences in this gradient. We did this by estimating the temperature dependences of bacterial growth, fungal growth and respiration. We determined the temperature sensitivity (Q<sub>10</sub>), the minimum temperature (T<sub>min</sub>) for growth and the optimum temperature (T<sub>opt</sub>) for growth. These metrics were then correlated to MAT. Additionally, we sequenced bacterial (16S) and fungal (ITS) amplicons from the different sites to also assess variance in community composition and structure. We hypothesized that microbes should be adapted to their historical temperature; microbial communities in warmer environments will be warm-shifted and vice versa.</p><p>We could effectively represent temperature relationships for bacterial growth, fungal growth, and respiration for all soils. As expected, temperature relationships correlated with the environmental temperature of the site, such that higher temperatures resulted in microbial communities with warm-adapted growth and respiration. This could be seen as a strong positive correlation between T<sub>min</sub> values and environmental temperatures which range from -14 to -5°C for bacteria, -11.5 to -4°C for fungi and -8 to -2°C for respiration. We found that MAT explains the microbial communities’ temperature dependencies for bacterial growth and respiration, but not for fungal growth. With 1°C rise in MAT, T<sub>min</sub> increased 0.17°C for bacterial growth, while T<sub>min</sub> for respiration increased by 0.11. Similarly, bacterial and fungal communities’ composition were correlated with MAT (r<sup>2</sup>=0.38; r<sup>2</sup>=0.62), and T<sub>min</sub> (r<sup>2</sup>=0.16; r<sup>2</sup>=0.21). These findings suggest that thermal adaptation occurs in processes such as bacterial growth and respiration, probably due to shifts in the microbial community composition. However, fungal growth seems to be less sensitive to changes in temperature, even though fungal communities’ composition was correlated with MAT.</p>

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 Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah I. Leichty ◽  
Christopher P. Kasanke ◽  
Sheryl L. Bell ◽  
Kirsten S. Hofmockel
Keyword(s):  
Microbial Communities ◽  
Soil Texture ◽  
Sandy Loam ◽  
Soil Microbial Communities ◽  
Cropping System ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Soil Microbial ◽  
Total Community ◽  
Rna And Dna

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

scholarly journals Soil microbial communities of three major Chinese truffles in southwest China

2016 ◽  
Vol 62 (11) ◽  
pp. 970-979 ◽  
Author(s):  
Yu Fu ◽  
Xiaolin Li ◽  
Qiang Li ◽  
Haowei Wu ◽  
Chuan Xiong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Southwest China ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Soil Microbial ◽  
Operational Taxonomic Units ◽  
Bacterial Genus ◽  
And Function ◽  
Arbuscular Mycorrhizal Fungal

Tuber pseudoexcavatum, Tuber sinoaestivum, and Tuber indicum are the 3 most important truffles growing in southeast China; however, their cultivation is still inefficient owing to the lack of understanding regarding the composition and function of the bacterial and fungal communities from the soils around the fruit bodies and the ectomycorrhiza of these truffles. The aim of this study was to disclose the microbial communities in truffle-producing soils in Huidong County, Sichuan, China, by using barcoded pyrosequencing. Approximately 350 000 quality-controlled sequences were obtained and grouped into 14 025 bacterial operational taxonomic units (OTUs) and 4385 fungal OTUs, which included 29 bacterial and 7 fungal phyla, respectively. The bacterial genus Acidobacterium and fungal genera Modicella, Pseudogymnoascus, and Mortierella were significantly more abundant in the control soils than in the truffle-producing soils (P < 0.05), while the bacterial genus Sphingomonas (Alphaproteobacteria) and arbuscular mycorrhizal fungal genus Glomus were significantly enriched in truffle-producing soil than in the control (P < 0.05), indicating their different roles within truffle grounds. Notably, some nonfungal organisms detected by 18S rDNA pyrosequencing were of high abundance, among which Cercozoa and Ochrophyta were significantly (P < 0.05) more abundant in truffle soils than in control soils, indicating their interactions with truffles.

Sign in / Sign up

Export Citation Format

Share Document