14 research outputs found

    Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

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    Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH(3) concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use

    The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol

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    Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in a subtropical Acrisol was studied in south Brazil. The plots at this site represent two tillage systems, two nitrogen fertilization regimes and three crop rotation systems. Using Illumina high-throughput sequencing of the 16S rRNA gene, the archaeal and bacterial composition was determined from phylum to species level in the different plot treatments. The relative abundance of these taxes was correlated with measured soil properties. The P, Mg, total organic carbon, total N and mineral N were significantly higher in the no-tillage system. The microbial diversity was higher in the no-tillage system at order, family, genus and species level. In addition, overall microbial composition changed significantly between conventional tillage and no-tillage systems. Anaerobic bacteria, such as clostridia, dominate in no-tilled soil as well as anaerobic methanogenic archaea, which were detected only in the no-tillage system. Microbial diversity was higher in plots in which only cereals (oat and maize) were grown. Soil management influenced soil biodiversity on Acrisol by change of composition and abundance of individual species

    Bioaugmentation-assisted phytoremediation of As, Cd, and Pb using Sorghum bicolor in a contaminated soil of an abandoned gold ore processing plant

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    The two main bottlenecks for a successful phytoremediation program are the metal availability in soil and the metal uptake and transfer to shoots of high biomass plants. Several agronomical practices have been tested to boost the bioavailability of metals in soils and accumulation in plants. Here we assessed the feasibility of plant-growth-promoting bacteria (PGPB) isolated from a site contaminated by gold ore processing activities to assist the phytoremediation of As, Cd, and Pb by Sorghum bicolor and mitigate the metal toxicity in plants. The bacteria Kluyvera intermedia, Klebsiella oxytoca, and Citrobacter murliniae were evaluated in single, double, and triple inoculations. They are regarded as metal resistant and were isolated from the rhizosphere of species naturally growing on the metal contaminated site. The treatments comprised two soils (contaminated and non-contaminated) and single (K. intermedia, K. oxytoca, or C. murliniae) or multiple inoculations (K. intermedia + K. oxytoca; K. intermedia + C. murliniae; K. oxytoca + C. murliniae; K. intermedia + K. oxytoca + C. murliniae). Plants were grown for 42 days after inoculation. The results showed that the PGPB K. oxytoca and the combination of K. intermedia + K. oxytoca and K. intermedia + C. murliniae were able to mitigate the metal toxicity in the contaminated soil and hence increase the shoot biomass, with implications to the effectiveness of phytoextraction. The sorghum ability to translocate Cd to shoots in the contaminated soil was enhanced through the single inoculation with K. oxytoca, C. murliniae, and K. oxytoca, as well as by the jointinoculation with K. oxytoca + C. murliniae, and K. intermedia + K. oxytoca + C. murliniae. Higher accumulation of metals in shoots is a crucial factor in successful phytoextraction. Arsenic and Pb, on the other hand, had their uptake and concentration in roots stimulated by the inoculation. Therefore, regarding these two metals, phytostabilization programs could benefit from the use of the bacteria studied here

    Components of the nitrogen metabolism of <i>Ca</i>. N. evergladensis

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    <p>: ammonia oxidation (4, 5), ammonia assimilation (8, 9, 10), nitrite reduction (6), nitrous oxide production (7). Reactions are mediated by the following transporters and enzymes: urea transporters, urease (1, 2), ammonia transporters (3), archaeal ammonia monooxygenase (AMO) (4), candidate enzyme: multicopper oxidase (5), nitrite reductase (NirK) (6), nitric oxide reductase (NorD, NorQ), catalytic subunit (NorB) is missing (7), glutamate dehydrogenase (8), glutamine synthetase (9), glutamate synthase (10). NO may upregulate activity of AMO. * - experimental evidences are needed.</p

    Comparison of protein coding sequences (CDS) of <i>Ca</i>. Nitrososphaera evergladensis with CDS of other ammonia-oxidizing archaea.

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    <p>(A) CDS of <i>Ca</i>. Nitrososphaera evergladensis were compared to CDS of <i>Ca</i>. N. gargensis. (B) CDS of the group I.1a (<i>N. maritimus</i>, <i>Ca</i>. N. sediminis, <i>C. symbiosum</i>, <i>Ca</i>. N. limnia, <i>Ca</i>. N. koreensis) were compared to CDS of the group I.1b (<i>Ca</i>. N. evergladensis and <i>Ca</i>. N. gargensis). Overlapping regions represent CDS with amino acid sequence identity 35% and higher.</p

    Genome synteny alignments of <i>Ca</i>. N. evergladensis, (A) <i>Ca</i>. N. gargensis and (B) <i>N. maritimus</i>.

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    <p>Axes X and Y represent topology of coding sequences in the comparing genomes. Entire genomes were compared by MUMmer 3.0 package using Promer tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101648#pone.0101648-Kurtz1" target="_blank">[114]</a>. Each dot represents a match of at least six amino acids from compared genomes. Forward matching amino acid sequences are plotted as red lines/dots while reverse are plotted as blue lines/dots. A line of dots with slope ‚Ää=‚Ää1 represents an undisturbed segment of conservation between the two sequences, while a line of slope ‚Ää=‚Ää‚ąí1 represents an inverted segment of conservation between the two sequences.</p

    A phylogenetic tree of ammonia-oxidizing archaea 16S rRNA gene sequences (about 1.4 kb).

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    <p>23 16S rRNA sequences of AOA were randomly selected from the National Center for Biotechnology Information databases. Conservative sites (1.08 kb) were selected using Gblocks. The branching patterns in the maximum-likelihood tree are denoted by their respective bootstrap values (1000 iterations).</p

    Genome Sequence of <i>Candidatus</i> Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

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    <div><p>The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon <i>Candidatus</i> Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The <i>de novo</i> assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. <i>Ca</i>. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative <i>Ca</i>. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.</p></div
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