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 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 ◽  
Yeast Genus ◽  
Soil Microbial ◽  
Physicochemical Factors ◽  
Microbial Community Structures ◽  
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 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 microbial communities and their correlation with environmental factors, and to compare microbial 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 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 ◽  
Yeast Genus ◽  
Soil Microbial ◽  
Physicochemical Factors ◽  
Microbial Community Structures ◽  
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 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 microbial communities and their correlation with environmental factors, and to compare microbial 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 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 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 Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

scholarly journals Erosion reduces soil microbial diversity, network complexity and multifunctionality

2021 ◽  
Author(s):  
Liping Qiu ◽  
Qian Zhang ◽  
Hansong Zhu ◽  
Peter B. Reich ◽  
Samiran Banerjee ◽  
...  
Keyword(s):  
Soil Erosion ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Negative Impact ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Relative Abundances ◽  
The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Jonathan R Gaiero ◽  
Micaela Tosi ◽  
Elizabeth Bent ◽  
Gustavo Boitt ◽  
Kamini Khosla ◽  
...  
Keyword(s):  
New Zealand ◽  
Acid Phosphatase ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Organic Phosphorus ◽  
Mineral Soil ◽  
Soil Microbial Communities ◽  
Organic P ◽  
Fungal Community Composition ◽  
Soil Microbial

ABSTRACT The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

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.

Sign in / Sign up

Export Citation Format

Share Document