Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species

343

157

Adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuum L.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with the Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes phyla. The relative abundance of members of the Bacteroidetes phylum increased from 12 to 30% as a result of biochar amendment, while that of the Proteobacteria decreased from 71 to 47%. The Bacteroidetes-affiliated Flavobacterium was the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total rootassociated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (Chitinophaga and Cellvibrio, respectively) and aromatic compound degraders (Hydrogenophaga and Dechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

“…4). Several Pseudoxanthomonas species are known opportunistic plant pathogens that are able to attack a diverse array of economically important crops (52).…”

Section: Resultsmentioning

confidence: 99%

Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

Kolton

Harel

Pasternak

et al. 2011

343

157

“…We found species of known plant pathogens, such as Pseudomonas syringae (58) and Pseudoxanthomonas spp. (59,60), in the rhizosphere of A. halleri grown on gamma-irradiated soil that showed a considerable lower relative sequence abundance in the untreated microcosms. However, further studies are necessary to identify the physiological response mechanisms induced by A. halleri grown on gamma-irradiated soil and to verify if pathogen control mechanisms provide a possible explanation for the lower Cd concentrations in A. halleri's green biomass after growth on gammairradiated soil.…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

Muehe

Weigold

Adaktylou

et al. 2015

129

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a "native" and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, "Candidatus Chloracidobacterium") of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. E levated metal concentrations in agricultural soils decrease the yield and quality of crops. One of these metals is cadmium (Cd), which is present in the waste materials and waters of many industries (1) and in phosphate fertilizers used in agriculture (2, 3). Besides causing a decrease in crop yield (4), Cd is also a risk to human health if larger quantities (Ͼ2.5 g kg Ϫ1 body weight week Ϫ1 , according to the EFSA [5]) are consumed (6-8). To preserve crop yield and quality, sustainable biotechnologies are urgently needed to relieve agricultural soils of metal contaminants. One promising soil remediation technology is phytoremediation-the use of plants for removing inorganic and organic contaminants from soils (9-11). Phytoremediation is attractive, as it is sustainable and relatively inexpensive compared to other soil cleanup strategies. So far, it has rarely been employed on the field scale (12) due to its low efficiency, slow progress, and the need to develop individual implementation strategies depending on the field site conditions and plant type.Arabidopsis halleri has been studied as a model plant for Cd as well as zinc (Zn) hyperaccumulation in order to apply the plant for phytoremediati...

“…Thauera, also isolated from the nearby Coleville field (13), and Azoarcus and Diaphorobacter couple reduction of nitrate to N 2 to oxidation of aromatics (19,32). Gammaproteobacterial hNRB included the genera Moritella, Pseudomonas, Pseudoxanthomonas, and Thermomonas (22,36,42). Denitrovibrio acetiphilus is one of few identified ammonium-generating hNRB (25).…”

Section: Discussionmentioning

confidence: 99%

Ammonium Concentrations in Produced Waters from a Mesothermic Oil Field Subjected to Nitrate Injection Decrease through Formation of Denitrifying Biomass and Anammox Activity

Shartau

Yurkiw

Lin

et al. 2010

Community analysis of a mesothermic oil field, subjected to continuous field-wide injection of nitrate to remove sulfide, with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes indicated the presence of heterotrophic and sulfide-oxidizing, nitrate-reducing bacteria (hNRB and soNRB). These reduce nitrate by dissimilatory nitrate reduction to ammonium (e.g., Sulfurospirillum and Denitrovibrio) or by denitrification (e.g., Sulfurimonas, Arcobacter, and Thauera). Monitoring of ammonium concentrations in producing wells (PWs) indicated that denitrification was the main pathway for nitrate reduction in the field: breakthrough of nitrate and nitrite in two PWs was not associated with an increase in the ammonium concentration, and no increase in the ammonium concentration was seen in any of 11 producing wells during periods of increased nitrate injection. Instead, ammonium concentrations in produced waters decreased on average from 0.3 to 0.2 mM during 2 years of nitrate injection. Physiological studies with produced waterderived hNRB microcosms indicated increased biomass formation associated with denitrification as a possible cause for decreasing ammonium concentrations. Use of anammox-specific primers and cloning of the resulting PCR product gave clones affiliated with the known anammox genera "Candidatus Brocadia" and "Candidatus Kuenenia," indicating that the anammox reaction may also contribute to declining ammonium concentrations. Overall, the results indicate the following: (i) that nitrate injected into an oil field to oxidize sulfide is primarily reduced by denitrifying bacteria, of which many genera have been identified by DGGE, and (ii) that perhaps counterintuitively, nitrate injection leads to decreasing ammonium concentrations in produced waters.