Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome

Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Maine through management of wild populations. Given the constraints of this cropping system, the application of fungicides is critical to reducing disease pressure and ensuring consistent yields. However, as plant health is intertwined with soil health, it is important to consider the impact of fungicides on microbial communities. To understand the effects of fungicides in this context, bacterial and fungal microbial communities from fungicide-treated plots, as well as untreated control plots (UTG) were analyzed using amplicon sequencing. The fungicides, considered collectively as a combined treatment group (CTG), lead to a loss in fungal richness. One family, Clavariaceae, had an increased abundance under prothioconazole relative to UTG. This finding may be significant as taxa in Clavariaceae have been thought to potentially form ericoid mycorrhizae with Vaccinium. Five functional pathways and 74 enzymes differed significantly in relative abundance between CTG and UTG including enzymes associated with soil nutrient cycles. Most notably, enzymes corresponding to the breakdown of halogen-organic compounds had an increased abundance in CTG, suggesting bacterial fungicide degradation. Some enzymes associated with soil nutrient cycles differed significantly, possibly implying changes to nutrient pathways due to fungicide treatment.

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Wine terroir and the soil microbiome: an amplicon sequencing–based assessment of the Barossa Valley and its sub-regions

10.1101/2020.08.12.246447 ◽

2020 ◽

Author(s):

Jia Zhou ◽

Timothy R. Cavagnaro ◽

Roberta De Bei ◽

Tiffanie M. Nelson ◽

John R. Stephen ◽

...

Keyword(s):

Microbial Communities ◽

Microbial Community Composition ◽

Geographic Distance ◽

Hypervariable Region ◽

Soil Microbial Communities ◽

Amplicon Sequencing ◽

Soil Microbiome ◽

Rrna Gene ◽

Wine Quality ◽

The Impact

AbstractSoil is an important factor that contributes to the uniqueness of a wine produced by vines grown in specific conditions. Recent data shows that the composition, diversity and function of soil microbial communities may play important roles in determining wine quality and indirectly affect its economic value. Here, we evaluated the impact of environmental variables on the soil microbiomes of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) caused more microbial dissimilarity than geographic distance. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in microbial community composition were significantly associated with differences in fruit traits and in wine chemical and metabolomic profiles, highlighting the potential influence of microbial communities on the phenotype of grapevines. Our results suggest that environmental factors affect wine terroir, and this may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil microbiomes.

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Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charles S. Cockell ◽

Bettina Schaefer ◽

Cornelia Wuchter ◽

Marco J. L. Coolen ◽

Kliti Grice ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Granitic Rocks ◽

Rrna Gene ◽

Deep Biosphere ◽

Deep Subsurface ◽

Cell Biomass ◽

Colonization Potential ◽

The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Foods ◽

10.3390/foods9091247 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1247

Author(s):

Emiel Van Reckem ◽

Christina Charmpi ◽

David Van der Veken ◽

Wim Borremans ◽

Luc De Vuyst ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Bacterial Communities ◽

Geographical Origin ◽

Salt Content ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Future Application ◽

Processing Conditions ◽

The Impact

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

10.21203/rs.3.rs-729563/v1 ◽

2021 ◽

Author(s):

Ying Zhang ◽

Yang Huo ◽

Zhiruo Zhang ◽

Suiyi Zhu ◽

Wei Fan ◽

...

Keyword(s):

Microbial Communities ◽

Northeast China ◽

Environmental Changes ◽

Quantitative Polymerase Chain Reaction ◽

Amplicon Sequencing ◽

Fecal Indicator ◽

16S Rrna Amplicon Sequencing ◽

Anthropogenic Inputs ◽

Wwtp Effluent ◽

The Impact

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

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Improvement of Soil Health and System Productivity through Crop Diversification and Residue Incorporation under Jute-Based Different Cropping Systems

Agronomy ◽

10.3390/agronomy11081622 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1622

Author(s):

Mukesh Kumar ◽

Sabyasachi Mitra ◽

Sonali Paul Mazumdar ◽

Bijan Majumdar ◽

Amit Ranjan Saha ◽

...

Keyword(s):

Cropping Systems ◽

Soil Health ◽

Cropping System ◽

Residue Management ◽

Soil Parameters ◽

Data Set ◽

System Productivity ◽

Sustainability Index ◽

Residue Incorporation ◽

The Impact

Crop diversity through residue incorporation is the most important method for sustaining soil health. A field study was conducted over five consecutive years (2012–2017) to see the impact of residue incorporartions in Inceptisol of eastern India. The main plot treatments had five cropping systems (CS), namely, fallow−rice−rice (FRR), jute−rice−wheat (JRW), jute−rice−baby corn (JRBc), jute−rice−vegetable pea (JRGp), jute−rice−mustard−mungbean/green gram (JRMMu), which cinsisted of four sub-plots with varied nutrient and crop residue management (NCRM) levels, namely crops with no residue +75% of the recommended dose of fertilizers (RDF) (F1R0), crops with the residue of the previous crops +75% RDF (F1R1), crops with no resiude +100% RDF (F2R0), and crops with residue +100% RDF (F2R1). The highest system productivity was obtained for JRBc (15.3 Mg·ha−1), followed by JRGp (8.81 Mg·ha−1) and JRMMu (7.61 Mg·ha−1); however, the highest sustainability index was found with the JRGp cropping system (0.88), followed by JRMMu (0.82). Among the NCRMs, the highest productivity (8.78 Mg·ha−1) and sustainability index (0.83) were recorded in F2R1. Five soil parameters, namely, bulk density, available K, urease activity, dehydrogenase activity, and soil microbial biomass carbon (SMBC), were used in the minimum data-set (MDS) for the calculation of the soil quality index (SQI). The best attainment of SQI was found in the JRGp system (0.63), closely followed by the JRMMu (0.61) cropping system.

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Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

10.1101/680694 ◽

2019 ◽

Author(s):

Sven P. Tobias-Hünefeldt ◽

Stephen R. Wing ◽

Nadjejda Espinel-Velasco ◽

Federico Baltar ◽

Sergio E. Morales

Keyword(s):

Community Structure ◽

New Zealand ◽

Microbial Communities ◽

National Park ◽

Amplicon Sequencing ◽

Forested Catchments ◽

Environmental Forcing ◽

Low Salinity ◽

The Impact ◽

Depth View

SummarySystems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

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Response of Soil Microbiome Structure to Biological Control Agents (BCAs) in Strawberry Greenhouse

10.1101/2020.12.24.424290 ◽

2020 ◽

Author(s):

Senlin Liu ◽

Muzammil Hassan Khan ◽

Zhongyuan Yuan ◽

Sarfraz Hussain ◽

Hui Cao ◽

...

Keyword(s):

Biological Control ◽

Microbial Community ◽

Fungal Pathogens ◽

Soil Health ◽

Amplicon Sequencing ◽

Soil Microbiome ◽

Continuous Cropping ◽

Biological Control Agents ◽

Land Utilization ◽

Effective Microorganisms

AbstractContinuous cropping always leads to severe abiotic and biotic problems, especially the high-intensity land utilization in greenhouses, which causes widespread concern. Effective Microorganisms (EM) and Bacillus subtilis (BS) have been widely used to promote plant growth and increase yields as biological control agents (BCAs). However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments by combining EM and BS with compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after the addition of EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Interestingly, both the relative abundance and FUNGuild predictions was consistent in revealing that BCAs may inhibit fungal pathogens in soils. Correlation analysis indicated that soil microbial community was indirectly driven by soil properties. Co-occurrence networks demonstrated that BCAs could be microecologically homogeneous through enhancing bacterial network complexity and modularity. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.

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Soil Health and Sustainable Agriculture

Sustainability ◽

10.3390/su12124859 ◽

2020 ◽

Vol 12 (12) ◽

pp. 4859 ◽

Cited By ~ 1

Author(s):

Monther M. Tahat ◽

Kholoud M. Alananbeh ◽

Yahia A. Othman ◽

Daniel I. Leskovar

Keyword(s):

Sustainable Agriculture ◽

Organic Farming ◽

Mycorrhizal Fungi ◽

Crop Production ◽

Management Practices ◽

Conservation Tillage ◽

Soil Health ◽

Soil Nutrient ◽

Labor Costs ◽

The Impact

A healthy soil acts as a dynamic living system that delivers multiple ecosystem services, such as sustaining water quality and plant productivity, controlling soil nutrient recycling decomposition, and removing greenhouse gases from the atmosphere. Soil health is closely associated with sustainable agriculture, because soil microorganism diversity and activity are the main components of soil health. Agricultural sustainability is defined as the ability of a crop production system to continuously produce food without environmental degradation. Arbuscular mycorrhizal fungi (AMF), cyanobacteria, and beneficial nematodes enhance water use efficiency and nutrient availability to plants, phytohormones production, soil nutrient cycling, and plant resistance to environmental stresses. Farming practices have shown that organic farming and tillage improve soil health by increasing the abundance, diversity, and activity of microorganisms. Conservation tillage can potentially increase grower’s profitability by reducing inputs and labor costs as compared to conventional tillage while organic farming might add extra management costs due to high labor demands for weeding and pest control, and for fertilizer inputs (particularly N-based), which typically have less consistent uniformity and stability than synthetic fertilizers. This review will discuss the external factors controlling the abundance of rhizosphere microbiota and the impact of crop management practices on soil health and their role in sustainable crop production.

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Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Journal of Fungi ◽

10.3390/jof7090686 ◽

2021 ◽

Vol 7 (9) ◽

pp. 686

Author(s):

María Julia Carbone ◽

Sandra Alaniz ◽

Pedro Mondino ◽

Matías Gelabert ◽

Ales Eichmeier ◽

...

Keyword(s):

Drought Stress ◽

Microbial Communities ◽

Community Dynamics ◽

Mycorrhizal Fungus ◽

Arbuscular Mycorrhizal ◽

Field Capacity ◽

Amplicon Sequencing ◽

Bulk Soil ◽

Foot Disease ◽

The Impact

Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO4 when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

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