Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates

AbstractBacterial and fungal communities of four pesticide rinsate treatment biobeds constructed in Alberta and Saskatchewan, Canada were profiled via high throughput DNA sequencing to assess the effect of biobed depth and pesticide application on microbial community composition. Biobeds differed in geographical location and biobed design, and composition of pesticide rinsates (including herbicides, fungicides, and insecticides). All biobeds achieved similar treatment efficacy and supported greater bacterial diversity relative to fungal diversity, yet selected for similar abundant bacterial orders of Actinomycetales, Acidobacteria, Rhizobiales, and Sphingobacteriales and fungal taxonomic groups of Dothideomycetes, Eurotiales, Hypocreales, and Sordariales. Biobeds differed in the presence of unique and differentiated genera and operational taxonomic units. Biobed depth did not uniformly impact the diversity and/or the microbial community structure. Overall, pesticide application increased bacterial diversity, but had limited effect on the more variable fungal diversity, therefore suggesting broader implication for the effect of applied fungicides on biobed fungal communities.HighlightsBiobeds support diverse bacterial and fungal communitiesSpecific “core” bacterial and fungal taxa are abundant in biobeds of different design and treatmentMicrobial diversity is not directly linked with pesticide type or diversity.

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Effects of plant cultivars on the structure of bacterial and fungal communities associated with ginseng

10.21203/rs.3.rs-50235/v1 ◽

2020 ◽

Author(s):

Huaying Wang ◽

Xiaoxue Fang ◽

Hao Wu ◽

Xinyu Cai ◽

Hongxing Xiao

Keyword(s):

Microbial Community ◽

Bacterial Communities ◽

Fungal Diversity ◽

Microbial Community Composition ◽

Fungal Communities ◽

Associated Bacteria ◽

Rhizosphere Microorganisms ◽

Soil Rhizosphere ◽

Bacteria And Fungi ◽

Rhizosphere Microbial Community

Abstract Background There is a growing awareness of the importance of root-associated bacteria and fungi to plant growth. At present, little is known about whether different ginseng cultivars affect the soil rhizosphere microbial community. Results Here, we examined the changes in the microorganismal diversity and composition of the rhizospheres of different ginseng cultivars. We found that fungal communities were more influenced by the cultivars than bacterial communities and revealed differences in the microbial community composition and diversity among the different ginseng cultivars. We found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ; however, TSBT had the lowest bacterial and fungal diversity. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the lifespan of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium spp. Conclusions Our results showed that the microbial diversity and community structures under different ginseng cultivars are significantly different and are related to the host cultivar. This result is helpful in providing information that could be used for the breeding of Panax ginseng.

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

10.7287/peerj.preprints.3288v1 ◽

2017 ◽

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ~20 and ~10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.

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Soil N2O emission potential falls along a denitrification phenotype gradient linked to differences in microbiome, rainfall and carbon availability

10.1101/2020.07.22.211268 ◽

2020 ◽

Author(s):

Matthew P. Highton ◽

Lars R. Bakken ◽

Peter Dörsch ◽

Steve Wakelin ◽

Cecile A. M. de Klein ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Ph Effect ◽

Microbial Community Composition ◽

16S Rrna Gene Sequencing ◽

N2o Emission ◽

Rrna Gene ◽

List Type ◽

Carbon Addition ◽

Carbon Availability

AbstractSoil denitrification produces the potent greenhouse gas nitrous oxide (N2O) and by further reduction of N2O, the harmless inert gas N2. N2O emission is determined by rate and timing of the N2O producing and reducing steps which are sensitive to a series of proximal and distal regulators such as pH and microbial community composition. Microbial community associations to N2O emission potential (N2O/(N2O+N2)) are commonly entangled with pH leaving the true role of community composition unclear. Here, we leverage a set of soil microbiomes strongly linked to rainfall above pH to test the hypothesis that microbiome vs. N2O emission potential (N2O/(N2O+N2)) correlations will be maintained across alternative distal drivers. N2O emission potential (N2O/(N2O+N2)) and denitrification gas (NO, N2O, N2) kinetics were assessed by automated gas chromatography while community composition was assessed by 16S rRNA gene sequencing and qPCR of nosZI and II genes. Analyses revealed a sustained correlation between microbiome and N2O emission potential (N2O/(N2O+N2)) in the absence of a pH effect. Further, a continuum of gas accumulation phenotypes linked to NO accumulation and sensitive to carbon addition are identified. Separate phenotypes carried out N2O production and reduction steps more concurrently or sequentially and thus determined N2O accumulation and emission potential (N2O/(N2O+N2)). Concurrent N2O producing/reducing soils typically contained NO accumulation to a low steady state, while carbon addition manipulations which increased NO accumulation also increased sequentiality of N2O production/reduction and thus emission potential (N2O/(N2O+N2)). These features may indicate a conserved NO inhibitory mechanism across multiple effectors (rainfall, community composition, carbon availability).HighlightsN2O emission potential is linked to microbiome changes associated with rainfall, but not to pH.Sequential vs. concurrent denitrification phenotypes differing in NO and N2O accumulation are identified.High N2O accumulation is associated with increased NO accumulation.Sequentiality of N2O production/reduction determines soil N2O emission potential.Sequentiality of N2O reduction was susceptible to manipulation via carbon addition.

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

10.7287/peerj.preprints.3288 ◽

2017 ◽

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

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Graphene oxide affects soil bacterial and fungal diversity even at parts-per-trillion concentrations

10.1101/530485 ◽

2019 ◽

Cited By ~ 1

Author(s):

Christian Forstner ◽

Thomas G. Orton ◽

Adam Skarshewski ◽

Peng Wang ◽

Peter M. Kopittke ◽

...

Keyword(s):

Carbon Nanotubes ◽

Graphene Oxide ◽

Ecosystem Services ◽

Microbial Communities ◽

Fungal Diversity ◽

Microbial Community Composition ◽

Fungal Communities ◽

Soil Microbial Diversity ◽

Soil Bacterial ◽

Over Time

AbstractGraphene oxide (GO) is an oxidized form of graphene that is relatively cheap and easy to produce. This has heralded its widespread use in a range of industries, with its likelihood of release into the environment increasing accordingly. In pure culture, GO has been shown to influence bacteria and fungi, but its effects on environmental microbial communities remain poorly characterized, despite the important ecosystem services that these organisms underpin. Here, we characterized the effects of GO and graphite, over time and at three concentrations (1 ng, 1 µg and 1 mg kg dry soil-1), on soil bacterial and fungal diversity using 16S rRNA and ITS2 gene amplicon sequencing. Graphite was included as a reference material as it is widely distributed in the environment. Neither GO or graphite had significant effects on the alpha diversity of microbial communities. The composition of bacterial and fungal communities, however, was significantly influenced by GO and graphite. These effects were equally apparent between doses and varied over time. Predicted KEGG pathways and fungal guild structures were not significantly influenced by the treatments. Our study demonstrates that GO can influence soil microbial diversity, even at parts-per-trillion concentration, which is equivalent to the rates of release predicted for similar nanomaterials such as carbon nanotubes.ImportanceGraphene oxide is a nanomaterial with broad and expanding industrial applications. Some evidence indicates that it can influence the growth of microorganisms, many of which support important ecosystem services, such as the provision of food and clean water. The amount of graphene oxide currently entering soils is not known but is likely to be similar to other nanomaterials, such as carbon nanotubes (i.e. parts-per-trillion to parts-per-billion per year). In this study, we demonstrate that graphene oxide added to soil at these concentrations (or higher) can alter the composition of bacterial and fungal communities. Nonetheless, we found that these changes were of similar magnitude to those associated with the addition of graphite, which is common and occurs naturally in soils. Further research is recommended to determine whether the changes in microbial community composition that we have shown can be induced by graphene oxide, have deleterious consequences for soil health.

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Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

PeerJ ◽

10.7717/peerj.3930 ◽

2017 ◽

Vol 5 ◽

pp. e3930 ◽

Cited By ~ 11

Author(s):

Craig Anderson ◽

Mike Beare ◽

Hannah L. Buckley ◽

Gavin Lear

Keyword(s):

Microbial Community ◽

Agricultural Soils ◽

Microbial Community Composition ◽

Chemical Properties ◽

Community Response ◽

Fungal Communities ◽

Physicochemical Changes ◽

Tillage Depth ◽

Tillage Treatment

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.

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Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil

PeerJ ◽

10.7717/peerj.8541 ◽

2020 ◽

Vol 8 ◽

pp. e8541

Author(s):

Zhigang An ◽

Fengxia Guo ◽

Yuan Chen ◽

Gang Bai ◽

Zhengjun Chen

Keyword(s):

Microbial Community ◽

Community Composition ◽

Significant Variation ◽

Microbial Community Composition ◽

Fungal Communities ◽

Environmental Drivers ◽

Angelica Sinensis ◽

Growth Stages ◽

Meadow Soil ◽

Plant Weight

Background Angelica sinensis seedlings are grown in alpine uncultivated meadow soil with rainfed agroecosystems to ensure the quality of A. sinensis after seedling transplantation. The aim was to investigate the rhizosphere bacterial and fungal communities during the growth stages of A. sinensis seedlings. Methods The bacterial and fungal communities were investigated by HiSeq sequencing of 16S and 18S rDNA, respectively. Results Proteobacteria and Bacteroidetes were bacterial dominant phyla throughout growth stages. Fungal dominant phyla varied with growth stages, dominant phyla Ascomycota and Chytridiomycota in AM5, dominant phyla Basidiomycota, Ascomycota and Zygomycota in BM5, and dominant phyla Basidiomycota and Ascomycota in CM5. There was no significant variation in the alpha-diversity of the bacterial and fungal communities, but significant variation was in the beta-diversity. We found that the variation of microbial community composition was accompanied by the changes in community function. The relative abundance of fungal pathogens increased with plant growth. We also identified the core microbes, significant-changing microbes, stage-specific microbes, and host-specific microbes. Plant weight, root length, root diameter, soil pH, rainfall, and climate temperature were the key divers to microbial community composition. Conclusions Our findings reported the variation and environmental drivers of rhizosphere bacterial and fungal communities during the growth of A. sinensis seedlings, which enhance the understanding of the rhizosphere microbial community in this habitat.

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