scholarly journals Nitrifying Microbes in the Rhizosphere of Perennial Grasses Are Modified by Biological Nitrification Inhibition

2020 ◽  
Vol 8 (11) ◽  
pp. 1687
Author(s):  
Yi Zhou ◽  
Christopher J. Lambrides ◽  
Jishun Li ◽  
Qili Xu ◽  
Ruey Toh ◽  
...  
Keyword(s):  
Cynodon Dactylon ◽  
Perennial Grasses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Nitrification Inhibition ◽  
Microbial Oxidation ◽  
Seashore Paspalum ◽  
Soil Nitrification ◽  
Biological Nitrification

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

scholarly journals The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 456 ◽  
Author(s):  
Massimiliano Cardinale ◽  
Stefan Ratering ◽  
Aitak Sadeghi ◽  
Sushil Pokhrel ◽  
Bernd Honermeier ◽  
...  
Keyword(s):  
N Fertilization ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Future Research ◽  
Arable Soils ◽  
Mineral N ◽  
Bacterial Microbiota

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

scholarly journals Biological nitrification inhibition and forage productivity of Megathyrsus maximus in Colombian dry tropics

2021 ◽  
Author(s):  
Juliana Carvajal-Tapia ◽  
Sandra Morales Velasco ◽  
Daniel M. Villegas ◽  
Jacobo Arango ◽  
Nelson José Vivas Quila
Keyword(s):  
Dry Matter ◽  
High Capacity ◽  
Quality Parameters ◽  
Nitrification Inhibition ◽  
Soil Nitrification ◽  
Nutrition Quality ◽  
Dry Tropics ◽  
Biological Nitrification ◽  
Grassland Production ◽  
Germplasm Accessions

Agronomic, nutritional, and environmental aspects are integrated to promote sustainable tropical grassland production. Biological nitrification inhibition (BNI) is a plant-based strategy to improve nitrogen use efficiency by grasses in which they suppress the pace of soil nitrification via exudation of inhibitory compounds. To evaluate the effect of BNI on the productive performance of Megathyrsus maximus under field conditions, we evaluated a collection of 27 germplasm accessions and commercial cultivars of the forage grass in the dry tropics of Colombia. We measured plant yield dry matter, nutrition quality parameters, and nitrification rates of soil at 22 months after pasture establishment. Our results highlighted germplasm accessions of superior agronomic performance (for dry matter production and nutrition quality) and high capacity to decrease nitrification. Although no relation was observed between agronomic aspects, nutritional aspects, and nitrification rates, we conclude that there is no agronomic or nutritional penalty on environmentally friendly grasses, and BNI could be adopted as a target trait in plant breeding programs toward the development of eco-efficient forages and contribute to the sustainable intensification of livestock systems.  

scholarly journals First Report of Meloidogyne marylandi Infecting Bermudagrass in Oklahoma

Plant Disease ◽  
2014 ◽  
Vol 98 (9) ◽  
pp. 1286-1286 ◽  
Author(s):  
N. Walker
Keyword(s):  
Cynodon Dactylon ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Similar Species ◽  
Root Knot Nematode ◽  
Putting Greens ◽  
Egg Masses ◽  
First Report ◽  
Mean Width ◽  
Ultradwarf Bermudagrass

Meloidogyne marylandi is a nematode commonly associated with turfgrasses and has been reported to occur in Texas and Arkansas (1,3). In the fall of 2013, a stand of ultradwarf bermudagrass (Cynodon dactylon × C. transvaalensis) plants in a sand-based, research putting green in Stillwater, Oklahoma, exhibited symptoms of decline. Roots of the affected plants had small galls and upon staining of the root system, numerous egg masses were evident. Egg masses were collected, placed in water, and the morphology of 20 hatched, second-stage juveniles were examined. The characteristics of the juveniles were: body length averaged 393.1 ± 19.87 (range: 361 to 425) μm, mean width averaged 16.6 ± 0.7 (15.6 to 17.8) μm, stylet lengths averaged 12.1 ± 0.7 (10.4 to 12.9) μm, dorsal gland orifice from stylet base averaged 2.9 ± 0.4 (2.5 to 3.6) μm, tail lengths averaged 53.7 ± 3.8 (46.2 to 60.4) μm, and the hyaline region of the tails averaged 10.4 ± 1.1 (8.4 to 12.7) μm. Genomic DNA was extracted from six females that were removed from roots. Amplification and sequencing of the mitochondrial DNA region between COII and 16S rRNA genes was performed with primers 1RNAF (5′-TACCTTTGACCAATCACGCT-3′) and CO11R (5′-GGTCAATGTTCAGAAATTTGTGG-3′) as previously described (2). A PCR product approximately 510 bp in length was obtained and sequenced at the Oklahoma State University Core Facility. Sequences were compared with those in NCBI's nucleotide database using BLAST and had 97% identity with two sequences from M. marylandi (KC473862.1 and KC473863.1) and the next most similar species being M. graminis (JN241898.1) with 83% identity. To our knowledge, this is the first report of the root-knot nematode M. marylandi in Oklahoma. As bermudagrass becomes more commonly used for putting greens in the turfgrass transition zone, M. marylandi may become a more common and damaging pathogen in the region. References: (1) A. A. Elmi et al. Grass For. Sci. 55:166, 2000. (2) M. A. McClure et al. Plant Dis. 96:635, 2012. (3) J. L. Starr et al. Nematrop. 37:43, 2007.

scholarly journals Compositional and functional profiling of the rhizosphere microbiomes of the invasive weed Ageratina adenophora and native plants

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10844
Author(s):  
Yun Xia ◽  
Minghua Dong ◽  
Lei Yu ◽  
Lingdong Kong ◽  
Robert Seviour ◽  
...  
Keyword(s):  
Plant Species ◽  
Mycorrhizal Fungi ◽  
Imperata Cylindrica ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Native Plant ◽  
Native Plant Species ◽  
Ageratina Adenophora ◽  
Relative Abundances

The rhizosphere soil microbiome (RSM) plays an important role in the nutritional metabolism of the exotic weed Ageratina adenophora. However, our understanding of the composition and metabolic activity of this microbiome is limited. We used high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer fragments in combination with transcriptome analysis to compare the composition and metabolic features of the RSMs of A. adenophora and the native plant species Artemisia indica and Imperata cylindrica. A. indica cohabitates with the weed and I. cylindrica grows in uninvaded soil areas. We found fungi belonging to the phyla Ascomycota and Basidiomycota and bacteria belonging to the phyla Proteobacteria, Acidobacteria and Bacteroidetes were highly abundant in the RSMs of A. adenophora and both native plant species. The RSM of A. adenophora differed to varying degrees in the relative abundances of bacterial and fungal phyla and genera, and in levels of expression of functional genes from those of both the native species. The RSM of A. adenophora was more metabolically active than both of these, as indicated by marked increases in the expression levels of genes associated with cell wall, membrane, and envelope biogenesis, energy production and conversion, and the transport and metabolism of carbohydrates, amino acids, coenzymes, nucleotides, and secondary metabolites. Ascomycota and Basidiomycota contributed most significantly to these differences. The composition and metabolic activities of A. adenophora RSM differed less to the RSM of A. indica than to the RSM of I. cylindrica. Fungal communities contributed most to the metabolic genes in the RSM of A. adenophora. These included the arbuscular mycorrhizal fungi Glomeromycota. The different relative abundances in the RSMs of these three plant populations may explain why A. adenophora is more successful in colonizing soils than the two native populations.

scholarly journals Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

2015 ◽  
Vol 81 (9) ◽  
pp. 3218-3227 ◽  
Author(s):  
Jun Zhao ◽  
Baozhan Wang ◽  
Zhongjun Jia
Keyword(s):  
High Throughput ◽  
Paddy Soil ◽  
Stable Isotope Probing ◽  
Paddy Fields ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Ammonia Oxidizing Bacteria ◽  
Soil Nitrification ◽  
Content Type

ABSTRACTPaddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaealamoAgene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance ofNitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), andNitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of13C-labeled DNA further revealed that13CO2was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA andNitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated withNitrosospirasp. strain L115 and theNitrosospira multiformislineage and that the13C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic “CandidatusNitrososphaera gargensis,” uncultured fosmid 29i4, and acidophilic “CandidatusNitrosotalea devanaterra” lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Coordination of microbe–host homeostasis by crosstalk with plant innate immunity

Nature Plants ◽  
2021 ◽  
Author(s):  
Ka-Wai Ma ◽  
Yulong Niu ◽  
Yong Jia ◽  
Jana Ordon ◽  
Charles Copeland ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Amplicon Sequencing ◽  
Host Susceptibility ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Root Growth Inhibition ◽  
Natural Soil ◽  
Molecular Pattern ◽  
Immune Related Genes ◽  
Molecular Patterns

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.

scholarly journals Comparison of oral microbiome profiles in 18-month-old infants and their parents

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryutaro Jo ◽  
Kazuma Yama ◽  
Yuto Aita ◽  
Kota Tsutsumi ◽  
Chikako Ishihara ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dental Caries ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Commensal Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Deciduous Dentition ◽  
The Difference ◽  
Generation Sequencing

AbstractThe onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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