scholarly journals Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

2018 ◽  
Author(s):  
Hirokazu Toju ◽  
Yu Tanaka
Keyword(s):  
Crop Production ◽  
High Throughput Sequencing ◽  
Infected Plant ◽  
Agricultural Practices ◽  
Root Knot Nematodes ◽  
Indigenous Resident ◽  
Agroecosystem Management ◽  
Soybean Plants ◽  
Bacteria And Fungi ◽  
Taxonomic Groups

AbstractCyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, as effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics, and agricultural practices, more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes [Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales), and Purpureocillium (Hypocreales)] co-occurred in the soybean rhizosphere at a small spatial scale. Overall, this study suggests how “consortia” of anti-nematode microbes can derive from indigenous (resident) microbiomes, thereby providing basic information for managing anti-nematode microbial communities in agroecosystems.

scholarly journals Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

2019 ◽  
Vol 6 (3) ◽  
pp. 181693 ◽  
Author(s):  
Hirokazu Toju ◽  
Yu Tanaka
Keyword(s):  
Crop Production ◽  
High Throughput Sequencing ◽  
Infected Plant ◽  
Agricultural Practices ◽  
Root Knot Nematodes ◽  
Indigenous Resident ◽  
Agroecosystem Management ◽  
Soybean Plants ◽  
Bacteria And Fungi ◽  
Taxonomic Groups

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes ( Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales) and Purpureocillium (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.

scholarly journals Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun Zhang ◽  
Pengcheng Xing ◽  
Mengyu Niu ◽  
Gehong Wei ◽  
Peng Shi
Keyword(s):  
High Throughput Sequencing ◽  
Niche Overlap ◽  
Spatial Location ◽  
Bulk Soil ◽  
Community Structures ◽  
Potential Predator ◽  
Predator Prey ◽  
Soybean Plants ◽  
Bacteria And Fungi ◽  
Potential Interactions

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R2 = 0.37–0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R2 = 0.08–0.09) or cultivar type (R2 = 0.02–0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

Comparative Advantage of Using Biopesticides in Ukrainian Agroecosystems

2020 ◽  
Vol 2 (6) ◽  
Author(s):  
Hasrat Arjjumend ◽  
Konstantia Koutouki ◽  
Olga Donets
Keyword(s):  
Shelf Life ◽  
Crop Production ◽  
Plant Protection ◽  
Agricultural Practices ◽  
Crop Productivity ◽  
Poor Quality ◽  
Soil Biology ◽  
Chemical Contamination ◽  
High Concentration ◽  
Irreversible Damage

The use of unsustainable levels of chemical fertilizers and plant protection chemicals has resulted in a steady decline in soil and crop productivity the world over. Soil biology has undergone irreversible damage, coupled with a high concentration of toxic chemical residues in plant tissues and human bodies. Agricultural practices must evolve to sustainably meet the growing global demand for food without irreversibly damaging soil. Microbial biocontrol agents have tremendous potential to bring sustainability to agriculture in a way that is safe for the environment. Biopesticides do not kill non-target insects, and biosafety is ensured because biopesticides act as antidotes and do not lead to chemical contamination in the soil. This article is part of a larger study conducted in Ukraine by researchers at the Université de Montréal with the support of Mitacs and Earth Alive Clean Technologies. The responses of farmers who use biofertilizers (“user farmers”) and those who do not (“non-user farmers”), along with the responses of manufacturers or suppliers of biofertilizers, and research and development (R&D) scientists are captured to demonstrate the advantages of applying microbial biopesticides to field crops. Participants reported a 15-30% increase in yields and crop production after the application of biopesticides. With the use of biopesticides, farmers cultivated better quality fruits, grains, and tubers with a longer shelf life. Moreover, while the risk of crop loss remains high (60-70%) with chemically grown crops, this risk is reduced to 33% on average if crops are grown using biopesticides. The findings indicate that a large proportion of farmers would prefer to use biopesticides if they are effective and high quality products. In this context, the quality and effectiveness of products is therefore very important. Despite their benefits to soil, human health, and ecosystems, biopesticides face significant challenges and competition vis-à-vis synthetic pesticides for a variety of reasons. Therefore, the development of biopesticides must overcome the problems of poor quality products, short shelf life, delayed action, high market costs, and legal/registration issues.

scholarly journals Microbial Biocontrol as an Alternative to Synthetic Fungicides: Boundaries between Pre- and Postharvest Applications on Vegetables and Fruits

Fermentation ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 60
Author(s):  
Vincenzo Michele Sellitto ◽  
Severino Zara ◽  
Fabio Fracchetti ◽  
Vittorio Capozzi ◽  
Tiziana Nardi
Keyword(s):  
Crop Production ◽  
Fruits And Vegetables ◽  
Control Plant ◽  
Agricultural Practices ◽  
Plant Diseases ◽  
Postharvest Quality ◽  
Crucial Point ◽  
Production Chain ◽  
Vegetables And Fruits ◽  
And Storage

From a ‘farm to fork’ perspective, there are several phases in the production chain of fruits and vegetables in which undesired microbial contaminations can attack foodstuff. In managing these diseases, harvest is a crucial point for shifting the intervention criteria. While in preharvest, pest management consists of tailored agricultural practices, in postharvest, the contaminations are treated using specific (bio)technological approaches (physical, chemical, biological). Some issues connect the ‘pre’ and ‘post’, aligning some problems and possible solution. The colonisation of undesired microorganisms in preharvest can affect the postharvest quality, influencing crop production, yield and storage. Postharvest practices can ‘amplify’ the contamination, favouring microbial spread and provoking injures of the product, which can sustain microbial growth. In this context, microbial biocontrol is a biological strategy receiving increasing interest as sustainable innovation. Microbial-based biotools can find application both to control plant diseases and to reduce contaminations on the product, and therefore, can be considered biocontrol solutions in preharvest or in postharvest. Numerous microbial antagonists (fungi, yeasts and bacteria) can be used in the field and during storage, as reported by laboratory and industrial-scale studies. This review aims to examine the main microbial-based tools potentially representing sustainable bioprotective biotechnologies, focusing on the biotools that overtake the boundaries between pre- and postharvest applications protecting quality against microbial decay.

scholarly journals Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge Domínguez ◽  
Manuel Aira ◽  
Keith A. Crandall ◽  
Marcos Pérez-Losada
Keyword(s):  
Sewage Sludge ◽  
Community Composition ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Agricultural Practices ◽  
Fungal Community Composition ◽  
Earthworm Casts ◽  
Composition And Structure ◽  
Sustainable Agricultural Practices

AbstractWastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal communities of earthworm casts were mainly composed of microbial taxa not found in the sewage sludge; thus most of the bacterial (96%) and fungal (91%) taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Upon completion of GAP and during CAP, modified microbial communities undergo a succession process leading to more diverse microbiotas than those found in sewage sludge. Consequently, bacterial and fungal community composition changed significantly during vermicomposting. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices, if heavy metals or other pollutants are under legislation limits or adequately treated.

scholarly journals Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 809
Author(s):  
Sen Wang ◽  
Wanyu Liu ◽  
Jun Li ◽  
Haotian Sun ◽  
Yali Qian ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Relative Abundance ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Fine Particulate Matter ◽  
Ecological Functions ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Variation Characteristics ◽  
Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

Exploiting the beneficial properties of microalgae for food and feed use

2021 ◽  
Vol 67 (4) ◽  
pp. 3634-3648
Author(s):  
Erika Koppányné Szabó ◽  
Krisztina Takács
Keyword(s):  
Climate Change ◽  
Crop Production ◽  
Raw Materials ◽  
Large Population ◽  
Agricultural Practices ◽  
Value Added ◽  
Biologically Active ◽  
Population Increase ◽  
Health Food ◽  
Food And Feed

By 2050, 9.8 billion people are projected to live on Earth, which means that we need to double our current food production to keep pace with such a large population increase. In addition, rising greenhouse gas emissions and the associated climate change are placing a significant strain on the planet’s ability to sustain itself. However, in order to increase the quantity of proteins of plant origin, it is necessary to increase crop production areas, harvesting frequencies and the quantity of crops produced. Unfortunately, the optimization of these factors is already very close to the available maximum in the current situation. The developed cultivation systems and maximum utilization of the soil power leads to very serious environmental problems, soil destruction, loss of biodiversity and serious environmental pollution through the transport of the produced plant raw materials. This poses a serious challenge to food security and further increases the risk of hunger. There is therefore a need for agricultural practices that can lead to the cultivation of food and feed crops that have better sustainability indicators and are more resilient to climate change, which can be used to safely produce health-promoting feeds, as well as novel and value-added foods. Within this group, a particular problem is presented by the protein supply of the population, as currently about one billion people do not have adequate protein intake. However, conventional protein sources are not sufficient to meet growing protein needs. As mentioned above, food and feed proteins are based on plant proteins. In recent years, a prominent role has been played by the research into alternative proteins and the mapping of their positive and negative properties. Among alternative proteins, special attention has been paid to various yeasts, fungi, bacteria, algae, singe cell proteins (SCPs) and insects. In this paper, we focus on the presentation of algae, particularly microalgae, which are of paramount importance not only because of their significant protein content and favorable amino acid composition, but also because they are also sources of many valuable molecules, such as polyunsaturated fatty acids, pigments, antioxidants, drugs and other biologically active compounds. It is important to learn about microalgae biomass in order to be able to develop innovative health food products.

scholarly journals Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

2017 ◽  
Vol 83 (22) ◽  
Author(s):  
Konstantia Gkarmiri ◽  
Shahid Mahmood ◽  
Alf Ekblad ◽  
Sadhna Alström ◽  
Nils Högberg ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stable Isotope ◽  
Oilseed Rape ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Stable Isotope Probing ◽  
Biofuel Production ◽  
Content Type ◽  
Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

scholarly journals Evaluation of the Relationship among Biogenic Amines, Nitrite and Microbial Diversity in Fermented Mustard

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6173
Author(s):  
Yangyang Yu ◽  
Lu Li ◽  
Yujuan Xu ◽  
Kejing An ◽  
Qiao Shi ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
High Throughput Sequencing ◽  
Starter Cultures ◽  
Sequencing Analysis ◽  
Maximum Residue Limit ◽  
Safety Standard ◽  
Bacteria And Fungi ◽  
High Level ◽  
Degradation Properties ◽  
The Relationship

Biogenic amines (BAs) and nitrites are both considered harmful compounds for customer health, and are closely correlated with the microorganisms in fermented mustard (FM). In this study, BAs and nitrite contents in fifteen FM samples from different brands were analyzed. The concentrations of cadaverine in one sample and of histamine in one sample were above the toxic level. Moreover, five FM samples contained a high level of nitrite, exceeding the maximum residue limit (20 mg/kg) suggested by the National Food Safety Standard. Then, this study investigated bacterial and fungal communities by high-throughput sequencing analysis. Firmicutes and Basidiomycota were identified as the major bacteria and fungi phylum, respectively. The correlations among microorganisms, BAs and nitrite were analyzed. Typtamine showed a positive correlation with Lactobacillus and Pseudomonas. Cadaverine and nitrite is positively correlated with Leuconostoc. Furthermore, thirteen strains were selected from the samples to evaluate the accumulation and degradation properties of their BAs and nitrite. The results indicated that the Lactobacillus isolates, including L. plantarum GZ-2 and L. brevis SC-2, can significantly reduce BAs and nitrite in FM model experiments. This study not only assessed the contents of BAs and nitrite in FM samples, but also provided potential starter cultures for BAs and nitrite control in the FM products industry.

scholarly journals Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

2021 ◽  
Vol 12 ◽  
Author(s):  
Junqing Luo ◽  
Zhechao Zhang ◽  
Yazhou Hou ◽  
Fengwei Diao ◽  
Baihui Hao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Salt Lake ◽  
Salinity Gradient ◽  
Salt Lakes ◽  
Hypersaline Environment ◽  
Hypersaline Lake ◽  
Littoral Zones ◽  
Microbial Resources ◽  
Bacteria And Fungi

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO42–, SOC, HCO3–, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

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