Micronutrients and Soil Microorganisms in the Suppression of Potato Common Scab

Nature-friendly approaches for crop protection are sought after in the effort to reduce the use of agrochemicals. However, the transfer of scientific findings to agriculture practice is relatively slow because research results are sometimes contradictory or do not clearly lead to applicable approaches. Common scab of potatoes is a disease affecting potatoes worldwide, for which no definite treatment is available. That is due to many complex interactions affecting its incidence and severity. The review aims to determine options for the control of the disease using additions of micronutrients and modification of microbial communities. We propose three approaches for the improvement by (1) supplying soils with limiting nutrients, (2) supporting microbial communities with high mineral solubilization capabilities or (3) applying communities antagonistic to the pathogen. The procedures for the disease control may include fertilization with micronutrients and appropriate organic matter or inoculation with beneficial strains selected according to local environmental conditions. Further research is proposed to use metagenomics/metabolomics to identify key soil–plant–microbe interactions in comparisons of disease-suppressive and -conducive soils.

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Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

Plant Disease ◽

10.1094/pdis-07-11-0571 ◽

2012 ◽

Vol 96 (5) ◽

pp. 718-725 ◽

Cited By ~ 97

Author(s):

Noah Rosenzweig ◽

James M. Tiedje ◽

John F. Quensen ◽

Qingxiao Meng ◽

Jianjun J. Hao

Keyword(s):

Microbial Communities ◽

Common Scab ◽

Disease Suppression ◽

Rrna Gene ◽

Suppressive Soil ◽

Streptomyces Spp ◽

Potato Common Scab ◽

Order Of Magnitude ◽

Disease Suppressive Soil ◽

Conducive Soil

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.

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Culture-Based Assessment of Microbial Communities in Soil Suppressive to Potato Common Scab

Plant Disease ◽

10.1094/pdis-05-11-0441 ◽

2012 ◽

Vol 96 (5) ◽

pp. 712-717 ◽

Cited By ~ 37

Author(s):

Qingxiao Meng ◽

Jingfang Yin ◽

Noah Rosenzweig ◽

David Douches ◽

Jianjun J. Hao

Keyword(s):

Microbial Communities ◽

Common Scab ◽

Fluorescent Pseudomonads ◽

Polymorphism Analysis ◽

Streptomyces Spp ◽

Restriction Fragment Polymorphism ◽

Potato Common Scab ◽

Total Fungi ◽

Total Bacteria ◽

Conducive Soil

A field in East Lansing, MI, showed a decline of potato common scab compared with an adjacent potato field. To confirm that the decline was due to biological factors, the soil was assayed. In the greenhouse, putative common-scab-suppressive soil (SS) was either treated with various temperatures or mixed with autoclaved SS at various ratios. Pathogenic Streptomyces scabies was incorporated into the treated soil at 106 CFU/cm3 of soil, followed by planting of either potato or radish. Disease severity was negatively correlated with the percentage of SS in the mixture and positively correlated with temperature above 60°C. The soil was screened for four groups of potential antagonists (general bacteria, streptomycetes, fluorescent pseudomonads, and bacilli) pairing in culture with S. scabies. The frequency of antagonistic bacteria in SS was higher than common-scab-conducive soil (CS) in all four groups but only pseudomonads and streptomycetes were significantly higher. The population of pathogenic Streptomyces spp. in the rhizosphere of CS was significantly higher than SS. Dilution plating of CS and SS samples showed no clear trends or differences in populations of total fungi, total bacteria, streptomycetes, fluorescent pseudomonads, and bacilli but terminal restriction fragment polymorphism analysis revealed two distinct microbial communities were present in SS and CS.

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Organoids to Dissect Gastrointestinal Virus–Host Interactions: What Have We Learned?

Viruses ◽

10.3390/v13060999 ◽

2021 ◽

Vol 13 (6) ◽

pp. 999

Author(s):

Sue E. Crawford ◽

Sasirekha Ramani ◽

Sarah E. Blutt ◽

Mary K. Estes

Keyword(s):

Cell Types ◽

Human Infection ◽

Viral Pathogens ◽

Host Interactions ◽

Complex Interactions ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Human Intestinal Epithelium ◽

Human Viruses ◽

Human Infections

Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

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Invasive plant-derived dissolved organic matter alters microbial communities and carbon cycling in soils

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2021.108191 ◽

2021 ◽

pp. 108191

Author(s):

Morgan Luce McLeod ◽

Lorinda Bullington ◽

Cory C. Cleveland ◽

Johannes Rousk ◽

Ylva Lekberg

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Microbial Communities ◽

Carbon Cycling ◽

Invasive Plant

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Differences in the Concentration and Composition of Human Milk Components Are Related to Variation in Milk and Infant Fecal Microbiomes

Current Developments in Nutrition ◽

10.1093/cdn/nzaa054_128 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1056-1056

Author(s):

Ryan Pace ◽

Janet Williams ◽

Kimberly Lackey ◽

Mark McGuire ◽

Michelle McGuire ◽

...

Keyword(s):

Human Milk ◽

Microbial Communities ◽

Infant Health ◽

Hypervariable Region ◽

Fecal Microbiota ◽

National Institutes Of Health ◽

Funding Sources ◽

Infant Feces ◽

Microbe Interactions ◽

Foundation Award

Abstract Objectives Profiles of human milk oligosaccharides (HMO) and milk/infant fecal microbiota vary globally. However, associations between and among HMO, other milk-borne factors (e.g., lactose, protein), and milk/infant fecal microbiomes have not been well-investigated. Here we tested the hypothesis that variations in milk lactose, protein, and HMO concentrations are associated with variations in the structure of milk and infant fecal microbial communities. Methods Milk/infant fecal samples from 357 maternal-infant dyads collected as part of the INSPIRE study from 11 geographically/culturally diverse sites located in eight countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and USA) were analyzed. DNA was extracted and bacterial 16S rRNA V1V3 hypervariable region amplified/sequenced for microbiome analysis. HMO, lactose, and protein profiles were generated from HPLC and spectrophotometric assays. Results Milk and infant feces share many of the same abundant bacterial genera, while also containing unique bacterial communities. Community states type (CST) analyses indicate both sample types group into a relatively small number of discrete communities characterized by enrichment of specific taxa (e.g., Streptococcus, Bifidobacterium). Concentrations of milk lactose and protein varied by population/CST. Additionally, variation in the microbial community structure of milk and infant feces was associated with concentrations of total/individual HMO, lactose, and protein. Conclusions Similar to HMO concentrations, milk lactose and protein vary globally. Variations in milk and infant fecal microbial communities are associated with those of milk lactose, protein, and HMO concentrations. Given these results, as well as prior data on the influence of other environmental variables (e.g., pumped vs. direct breastfeeding), additional longitudinal studies are needed to better understand this complex network of maternal-infant-microbe interactions with respect to environmental factors and how differences impact postnatal maternal-infant health. Funding Sources National Science Foundation (award 1,344,288), National Institutes of Health (R01 HD092297), and USDA.

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Assimilation of CO2 by soil microorganisms and transformation into soil organic matter

Organic Geochemistry ◽

10.1016/j.orggeochem.2004.05.001 ◽

2004 ◽

Vol 35 (9) ◽

pp. 1015-1024 ◽

Cited By ~ 71

Author(s):

Anja Miltner ◽

Hans-Hermann Richnow ◽

Frank-Dieter Kopinke ◽

Matthias Kästner

Keyword(s):

Organic Matter ◽

Soil Organic Matter ◽

Soil Microorganisms

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The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa056 ◽

2020 ◽

Vol 96 (6) ◽

Cited By ~ 3

Author(s):

A Katsoula ◽

S Vasileiadis ◽

M Sapountzi ◽

Dimitrios G Karpouzas

Keyword(s):

Microbial Communities ◽

Agricultural Production ◽

Soil Microorganisms ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Similar Response ◽

Repeated Application ◽

Plant Leaves ◽

Soil System ◽

Plant Soil

ABSTRACT Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant–soil system and agricultural production.

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Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter

Limnology and Oceanography ◽

10.4319/lo.2003.48.4.1608 ◽

2003 ◽

Vol 48 (4) ◽

pp. 1608-1617 ◽

Cited By ~ 169

Author(s):

Stuart E. G. Findlay ◽

Robert L. Sinsabaugh ◽

William V. Sobczak ◽

M. Hoostal

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Microbial Communities ◽

Structural Response

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Soil microbial biomass—Interpretation and consideration for soil monitoring

Soil Research ◽

10.1071/sr10203 ◽

2011 ◽

Vol 49 (4) ◽

pp. 287 ◽

Cited By ~ 52

Author(s):

V. Gonzalez-Quiñones ◽

E. A. Stockdale ◽

N. C. Banning ◽

F. C. Hoyle ◽

Y. Sawada ◽

...

Keyword(s):

Organic Matter ◽

Microbial Biomass ◽

Soil Microorganisms ◽

Soil Microbial Biomass ◽

Biological Function ◽

Anthropogenic Change ◽

Soil Monitoring ◽

Soil Microbial ◽

Quality Assessments ◽

The Impact

Since 1970, measurement of the soil microbial biomass (SMB) has been widely adopted as a relatively simple means of assessing the impact of environmental and anthropogenic change on soil microorganisms. The SMB is living and dynamic, and its activity is responsible for the regulation of organic matter transformations and associated energy and nutrient cycling in soil. At a gross level, an increase in SMB is considered beneficial, while a decline in SMB may be considered detrimental if this leads to a decline in biological function. However, absolute SMB values are more difficult to interpret. Target or reference values of SMB are needed for soil quality assessments and to allow ameliorative action to be taken at an appropriate time. However, critical values have not yet been successfully identified for SMB. This paper provides a conceptual framework which outlines how SMB values could be interpreted and measured, with examples provided within an Australian context.

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A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology

mSystems ◽

10.1128/msystems.00146-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 4

Author(s):

Kevin D. Kohl

Keyword(s):

Microbial Communities ◽

Vertical Integration ◽

Temporal Integration ◽

Data Sets ◽

Grand Challenges ◽

Animal Physiology ◽

Physiological Processes ◽

Microbe Interactions ◽

Animal Hosts ◽

Host Microbe Interactions

ABSTRACTInteractions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change. Addressing these challenges will require the use of a variety of animal models and the development of systems approaches that can integrate large, multiomic data sets from both microbial communities and animal hosts. Integrating host-microbe interactions into the established field of comparative physiology represents an exciting frontier for both fields.

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