scholarly journals Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sally Hilton ◽  
Emma Picot ◽  
Susanne Schreiter ◽  
David Bass ◽  
Keith Norman ◽  
...  
Keyword(s):  
Crop Yield ◽  
Oilseed Rape ◽  
Relative Abundance ◽  
Real World ◽  
Rhizosphere Soil ◽  
Rotation Frequency ◽  
Landscape Scale ◽  
Vital Role ◽  
Agricultural Systems ◽  
Yield Decline

Abstract Background The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK’s third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers’ fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. Results We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition. Conclusions We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield.

scholarly journals Effects of Long-Term Straw Management and Potassium Fertilization on Crop Yield, Soil Properties and Microbial Community in a Rice–Oilseed Rape Rotation

Agriculture ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1233
Author(s):  
Jifu Li ◽  
Guoyu Gan ◽  
Xi Chen ◽  
Jialong Zou
Keyword(s):  
Organic Carbon ◽  
Soil Properties ◽  
Crop Yield ◽  
Oilseed Rape ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
Crop Straw ◽  
K Fertilizer ◽  
Straw Incorporation

The present study aims to assess the influences of long-term crop straw returning and recommended potassium fertilization on the dynamic change in rice and oilseed rape yield, soil properties, bacterial and fungal alpha diversity, and community composition in a rice–oilseed rape system. A long-term (2011–2020) field experiment was carried out in a selected paddy soil farmland in Jianghan Plain, central China. There were four treatments with three replications: NP, NPK, NPS, and NPKS, where nitrogen (N), phosphate (P), potassium (K), and (S) denote N fertilizer, P fertilizer, K fertilizer, and crop straw, respectively. Results showed that long-term K fertilization and crop straw returning could increase the crop yield at varying degrees for ten years. Compared with the NP treatment, the long-term crop straw incorporation with K fertilizer (NPKS treatment) was found to have the best effect, and the yield rates increased by 23.0% and 20.5% for rice and oilseed rape, respectively. The application of NPK fertilizer for ten years decreased the bacterial and fungal alpha diversity and the relative abundance of dominant bacterial and fungal taxa, whereas continuous straw incorporation had a contradictory effect. NPKS treatment significantly increased the relative abundance of some copiotrophic bacteria (Firmicutes, Gemmatimonadetes, and Proteobacteria) and fungi (Ascomycota). Available K, soil organic matter, dissolved organic carbon, and easily oxidized organic carbon were closely related to alterations in the composition of the dominant bacterial community; easily oxidized organic carbon, dissolved organic carbon, and slowly available K were significantly correlated with the fungal community. We conclude that long-term crop straw returning to the field accompanied with K fertilizer should be employed in rice-growing regions to achieve not only higher crop yield but also the increase in soil active organic carbon and available K content and the improvement of the biological quality of farmland.

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 Diversity, Abundance, and Foraging Behavior of Ants (Hymenoptera: Formicidae) Scavenging on American Cockroach in Various Habitats of Nasarawa State, Nigeria

2020 ◽  
Vol 43 (4) ◽  
Author(s):  
Mohammed Ahmed Ashigar ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Rural Communities ◽  
Relative Abundance ◽  
Periplaneta Americana ◽  
Vital Role ◽  
American Cockroach ◽  
Conservation Implications ◽  
Residential Communities ◽  
Food Borne ◽  
Significant Difference ◽  
Paratrechina Longicornis

Ants play a vital role in removing dead arthropods from the environment. Complex foraging patterns are used by ants to locate food items and overwhelm even larger insects such as cockroach. Consequently, the biotic interaction between the ants and the American cockroach, Periplaneta americana, another home infesting and a vector of major food-borne diseases, may lead to microbial handover and ease the spread of mechanically transmitted human pathogenic microbes. This study was done to determine the diversity and abundance of cockroach-foraging ants in Nasarawa State, Nigeria. Ten households were randomly selected from 14 locations: 5 residential communities from three most urbanized areas (Lafia, Akwanga, and Keffi) and 5 rural communities. Four remaining locations were nonresidential from Lafia and Akwanga, respectively. A total of 1,364 ants belonging to three subfamilies (Myrmicinae, Formicinae, and Ponerinae) were collected from 140 households. Pheidole rugaticeps Emery recorded the highest relative abundance (52%) followed by Pheidole decarinata Santschi (16%), Pheidole sp. (17%), Camponotus maculatus (7%), Paratrechina longicornis (7%), while both Crematogaster sp. and Brachyponera sennaarensis recorded the lowest relative abundance (1%). There is a significant difference in the species diversity between the urban and the rural communities. Pheidole rugaticeps, P. decarinata, Pheidole sp., and P. longicornis were more organized in foraging and operating in group by recruiting nest-mate for collecting fragments of dead cockroach. Studies on the epidemiology, conservation implications, and biocontrol potentials of these Pheidole species are recommended.

scholarly journals Effects of continuous cropping of Pinellia ternata (Thunb.) Breit. on soil physicochemical properties, enzyme activities, microbial communities and functional genes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yuan Zhao ◽  
Xiao–Meng Qin ◽  
Xue–Ping Tian ◽  
Tao Yang ◽  
Rong Deng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Soil Fertility ◽  
Phenolic Acids ◽  
Relative Abundance ◽  
Enzyme Activities ◽  
Rhizosphere Soil ◽  
Functional Genes ◽  
Continuous Cropping ◽  
Pinellia Ternata

Abstract Background Pinellia ternata (Thunb.) Breit. is a commonly used herb in traditional Chinese medicine, and the main raw material of various Chinese patent medicines. Continuous cropping obstacle (CCO) is the main factor leading to the decline of crop yields and quality. Methods Metagenomics sequencing technology was used to analyze the microbial community and functional genes of continuous cropping (CC) and control (CK) soils of P. ternata. In addition, differences in physicochemical properties, enzyme activities, microbial community composition and the abundance of functional genes in CC and CK were evaluated, as well as the relationship between these factors and CCO. Results Results indicated that CC of P. ternata led to the decline of rhizosphere soil pH, nutrient imbalance and enzyme activity reduction. Metagenomic analysis indicted that CC also changed the composition of the microbial community, causing an increase in the relative abundance of pathogenic microorganisms such as Fusarium, Klebsiella oxytoca and Pectobacterium carotovorum in the P. ternata rhizosphere. The relative abundance of potentially beneficial Burkholderia and Bradyrhizobium was recorded to decrease. Results also showed that there were considerable differences in CC and CK about the abundances of functional genes related to soil enzymes and the degradation of P. ternata allelochemicals, as well as the microbial groups which they belong. These results clarified the effects of CC on the microbial community structure and functional genes of soil. In addition, Burkholderia and Bradyrhizobium might play important roles in enhancing soil fertility and reducing the toxicity of phenolic acids in rhizosphere soil. Conclusions CC of P. ternata changed the physicochemical properties, microbial community and functional genes of rhizosphere soil. Burkholderia and Bradyrhizobium for enhancing soil fertility and reducing the toxicity of phenolic acids might be potentially beneficial. These results provide theoretical guidance for bioremediation of CCO soil of P. ternata and other staple crops. Graphic abstract

scholarly journals Map Reduce Based Optimized Frequent Subgraph Mining Algorithm for Large Graph Database

2020 ◽  
Vol 9 (3) ◽  
pp. 3131-3139
Keyword(s):  
Distributed System ◽  
Real World ◽  
Transportation Network ◽  
Vital Role ◽  
Graph Database ◽  
Frequent Subgraph Mining ◽  
Large Graph ◽  
Subgraph Mining ◽  
Frequent Subgraph ◽  
Centralized System

Distributed System, plays a vital role in Frequent Subgraph Mining (FSM) to extract frequent subgraph from Large Graph database. It help to reduce in memory requirements, computational costs as well as increase in data security by distributing resources across distributed sites, which may be homogeneous or heterogeneous. In this paper, we focus on the problem related complexity of data arises in centralized system by using MapReduce framework. We proposed a MapReduced based Optimized Frequent Subgrph Mining (MOFSM) algorithm in MapReduced framework for large graph database. We also compare our algorithm with existing methods using four real-world standard datasets to verify that better solution with respect to performance and scalability of algorithm. These algorithms are used to extract subgraphs in distributed system which is important in real-world applications, such as computer vision, social network analysis, bio-informatics, financial and transportation network.

scholarly journals Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Stefanie P Glaeser ◽  
Iulian Gabur ◽  
Hossein Haghighi ◽  
Jens-Ole Bartz ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Quantitative Resistance ◽  
Bacterial Community Composition ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Host Genotype ◽  
Brassica Napus L ◽  
Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

scholarly journals TO CONTROL OR NOT TO CONTROL: HOW DO WE LEARN MORE ABOUT HOW AGRONOMIC INNOVATIONS PERFORM ON FARMS?

2017 ◽  
Vol 55 (S1) ◽  
pp. 303-309 ◽  
Author(s):  
RIC COE ◽  
JOYCE NJOLOMA ◽  
FERGUS SINCLAIR
Keyword(s):  
Crop Yield ◽  
Real World ◽  
Crop Management ◽  
Maize Yield ◽  
Scaling Up ◽  
System Response ◽  
Main Concern ◽  
The Real ◽  
Important Variation ◽  
The Impact

SUMMARYOur paper ‘Loading the dice in favour of the farmer: reducing the risk of adopting agronomic innovations’ revealed mean increases but also large variation in the impact of four agroforestry practises on maize yield, as experienced by farmers in Malawi. This prompted a response from Sileshi and Akinnifesi that was critical of the data and methods used. Their main concern was that farmers did not necessarily manage crops identically in plots with and those without trees, so the yield differences that we measured may be partly caused by these differences in crop management. We argue here that it is valid and useful to look at the actual effect on crop yield of farmers having trees intercropped with maize, rather than controlling for how the crop is managed, because this is what happens in the real world. Farmers respond to having trees in their field by treating their crop differently, so this is part of the system response to having trees in fields. Attempts to eliminate this will result in measuring an artefact rather than the real impact of trees on crop yield. By doing this, we revealed important variation in the impact of trees on crop yield amongst farmers, and we argue that it is important to explore, assess and communicate to farmers and development actors the extent and implications of this variation. Understanding the contextual factors that determine who is likely to benefit most from an innovation and for whom it is less suitable can then be incorporated in scaling up, so that targeting of innovations and the appropriateness of messages given to farmers are continuously refined.

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