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.

Comparisons of Soil Microbial Communities Influenced by Soil Texture, Nitrogen Fertility, and Rotations

Soil Science ◽  
2011 ◽  
Vol 176 (9) ◽  
pp. 487-494 ◽  
Author(s):  
Bruce A. Roberts ◽  
Felix B. Fritschi ◽  
William R. Horwath ◽  
Kate M. Scow ◽  
William D. Rains ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Texture ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Nitrogen Fertility

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 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.

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities

2020 ◽  
pp. 103834
Author(s):  
Olabiyi Obayomi ◽  
Mitiku Mihiret Seyoum ◽  
Lusine Ghazaryan ◽  
Christoph C. Tebbe ◽  
Jun Murase ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Texture ◽  
Irrigation Water ◽  
Soil Microbial Communities ◽  
Water Type ◽  
Soil Microbial

scholarly journals An Examination of Soil Microbial Communities and Litter Decomposition in Five Urban Land Uses in Metropolitan Milwaukee, WI, U.S.

2016 ◽  
Vol 42 (1) ◽  
Author(s):  
Keith Turnquist ◽  
Les Werner ◽  
Brian Sloss
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
C:N Ratio ◽  
Soil Microbial Communities ◽  
Urban Land ◽  
Land Uses ◽  
Fungal Community Composition ◽  
Soil Microbial ◽  
Physical And Chemical

The process of urbanization may alter the ability of microorganisms to supply nutrients to plants. However, both the composition and structure of soil biological communities, and the extent of variation within these communities, is not clear in urban areas. Therefore, baseline information regarding the impact of urban land management practices on soil microbial communities is essential to improving individuals’ ability to manage urban soils and the plants they support. This study examined soil microbial communities over five urban land uses with different degrees of urbanization in metropolitan Milwaukee, Wisconsin, U.S. The objectives were to 1) determine if differences exist in bacterial and fungal community composition, biological activity, and the soil physical and chemical environment across five urban land uses, and 2) determine if differences in the bacterial and fungal compositions compare to differences in the soil’s physical and chemical characteristics. Bulk density, soil organic matter, pH, magnesium, sodium, total nitrogen, and C:N ratio displayed significant differences between streets and forests. Microbial biomass did not differ between land uses, and the differences in bacterial and fungal community composition reflect only a small portion of the total microbial pool. The decomposition of transposed leaf litter showed significant decline in C:N ratio over time, but no statistical differences between land use were observed. The results display a highly redundant microbial assemblage, and suggest that in locations with adequate levels of soil carbon and where parent material and soil forming processes are homogeneous, urbanization and landscape management have less impact on soil microbiology than expected.

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