Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation

Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. Nevertheless, the molecular mechanisms controlling the feedback between root architecture and microbial community structure remain elusive in maize. Here, we demonstrate that transcriptomic gradients along the longitudinal root axis associate with specific shifts in rhizosphere microbial diversity. Moreover, we have established that root-derived flavones predominantly promote the enrichment of bacteria of the taxa Oxalobacteraceae in the rhizosphere, which in turn promote maize growth and nitrogen acquisition. Genetic experiments demonstrate that LRT1-mediated lateral root development coordinates the interactions of the root system with flavone-dependent Oxalobacteraceae under nitrogen deprivation. In summary, these experiments reveal the genetic basis of the reciprocal interactions between root architecture and the composition and diversity of specific microbial taxa in the rhizosphere resulting in improved plant performance. These findings may open new avenues towards the breeding of high-yielding and nutrient-efficient crops by exploiting their interaction with beneficial soil microorganisms.

Microbial Species Coexistence Depends on the Host Environment

Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germfree hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial distribution of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the relative abundances of both species on the host do not match the relative abundances reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems.IMPORTANCE This work studies microbial interactions within the microbiome of the simple cnidarian Hydra and investigates whether microbial species coexistence and community stability depend on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydra's microbiome differs depending on the environment and results in a stable coexistence only in the host context. The interactive ecology between the host and the two most dominant microbes, but also the less abundant members of the microbiome, is critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law

Beer's Law explains how light attenuates into thick specimens, including thick biofilms. We use a Bayesian optimality criterion, the maximum of the posterior probability distribution, and computationally efficiently fit Beer's Law to the 3D intensity data collected from thick living biofilms by a confocal scanning laser microscope. Using this approach the top surface of the biofilm and an optimal image threshold can be estimated. Biofilm characteristics, such as bio-volumes, can be calculated from this surface. Results from the Bayesian approach are compared to other approaches including the method of maximum likelihood or simply counting bright pixels. Uncertainty quantification (i.e., error bars) can be provided for the parameters of interest. This approach is applied to confocal images of stained biofilms of a common lab strain of Pseudomonas aeruginosa, stained biofilms of Janthinobacterium isolated from the Antarctic, and biofilms of Staphylococcusaureus that have been genetically modified to fluoresce green.

The effective migration of Massilia sp. WF1 by Phanerochaete chrysosporium and its phenanthrene biodegradation in soil

Pollutant-degrading bacteria migrated by fungi may enhance the contacts between microorganisms and pollutants and improve the bioremediation efficiency of persistent organic pollutants in soil. Here, the migration of phenanthrene (PHE)-degrading bacteria Massilia sp. WF1 and Mycobacterium sp. WY10 by the hydrophobic fungi Phanerochaete chrysosporium (P. chrysosporium) and its effects on the PHE biodegradation in soil were investigated. Migration of the hydrophilic bacterium WF1 was better than that of the hydrophobic bacterium WY10 by P. chrysosporium mycelia since strain WF1 possesses flagellum and the type III secretion system. The interaction energy change of P. chrysosporium-WF1 was lower, but the interaction forces (van der Waals attractions, capillary forces, and cross-linking effects) were stronger than those of P. chrysosporium-WY10. Thus, the adhesive attraction between strain WF1 and P. chrysosporium was stronger, and consequently, strain WF1 was migrated by P. chrysosporium to a greater extent than WY10. The corresponding migration mechanism was inferred to be a bacterial 'passive' method: bacteria adhered to mycelia before they migrated with the growing mycelia. Moreover, migrated strain WF1 via P. chrysosporium showed effective PHE biodegradation in soil. Fungus-mediated migration of pollutant-degrading bacteria may play an important role in the bioremediation of pollutants in soil.

Oxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas?

Mycophagous (=fungus feeding) soil bacteria of the genus Collimonas have been shown to colonize and grow on hyphae of different fungal hosts as the only source of energy and carbon. The ability to exploit fungal nutrient resources might require a strategy for collimonads to sense fungi in the soil matrix. Oxalic acid is ubiquitously secreted by soil fungi, serving different purposes. In this study, we investigated the possibility that collimonads might use oxalic acid secretion to localize a fungal host and move towards it. We first confirmed earlier indications that collimonads have a very limited ability to use oxalic acid as growth substrate. In a second step, with using different assays, we show that oxalic acid triggers bacterial movement in such a way that accumulation of cells can be expected at micro-sites with high free oxalic acid concentrations. Based on these observations we propose that oxalic acid functions as a signal molecule to guide collimonads to hyphal tips, the mycelial zones that are most sensitive for mycophagous bacterial attack.

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system

Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this might have on drinking water quality.

Geosmin degradation by seasonal biofilm from a biological treatment facility

INTRODUCTION

Initial geosmin degradation was closely related to water temperature and natural geosmin concentration of sampling environment. Here, for the first time, we evaluated the biodegradation of geosmin by microorganisms in biofilm from biological treatment unit of actual potable water treatment plant.

MATERIALS AND METHODS

At an initial geosmin concentration of 2,500 ng/l, efficient geosmin removal was confirmed throughout the year. Furthermore, in the presence of mixed musty odor compounds (geosmin and MIB) as carbon source, geosmin degradation was enhanced compared to sole carbon source (geosmin alone).

RESULTS AND DISCUSSION

PCR-DGGE analysis revealed a rich community structure within the biofilm during rapid geosmin removal period, April. PCA revealed that the significant change in bacterial communities occurred from day 1 to day 2. Two novel geosmin-degrading bacteria were isolated from the biofilm of the biological treatment unit of Kasumigaura Water Purification, Waterworks Department, Japan. They belong to Methylobacterium sp. and Oxalobacteraceae bacterium, respectively.

CONCLUSIONS

These studies provide further insights into the unknown microbiological processes that occur during the biological removal of geosmin through water treatment and could facilitate the geosmin bioremediation in contaminated habitats.

Towards a better understanding of the use of probiotics for preventing chytridiomycosis in Panamanian golden frogs

Populations of native Panamanian golden frogs (Atelopus zeteki) have collapsed due to a recent chytridiomycosis epidemic. Reintroduction efforts from captive assurance colonies are unlikely to be successful without the development of methods to control chytridiomycosis in the wild. In an effort to develop a protective treatment regimen, we treated golden frogs with Janthinobacterium lividum, a skin bacterium that has been used to experimentally prevent chytridiomycosis in North American amphibians. Although J. lividum appeared to colonize A. zeteki skin temporarily, it did not prevent or delay mortality in A. zeteki exposed to Batrachochytrium dendrobatidis, the causative agent of chytridiomycosis. After introduction of J. lividum, average bacterial cell counts reached a peak of 1.7 × 10(6) cells per frog ~2 weeks after treatment but declined steadily after that. When J. lividum numbers declined to ~2.8 × 10(5) cells per frog, B. dendrobatidis infection intensity increased to greater than 13,000 zoospore equivalents per frog. At this point, frogs began to die of chytridiomycosis. Future research will concentrate on isolating and testing antifungal bacterial species from Panama that may be more compatible with Atelopus skin.

Effect of arsenite on swimming motility delays surface colonization in Herminiimonas arsenicoxydans

Herminiimonas arsenicoxydans is a Gram-negative bacterium able to detoxify arsenic-contaminated environments by oxidizing arsenite [As(III)] to arsenate [As(V)] and by scavenging arsenic ions in an extracellular matrix. Its motility and colonization behaviour have been previously suggested to be influenced by arsenite. Using time-course confocal laser scanning microscopy, we investigated its biofilm development in the absence and presence of arsenite. Arsenite was shown to delay biofilm initiation in the wild-type strain; this was partly explained by its toxicity, which caused an increased growth lag time. However, this delayed adhesion step in the presence of arsenite was not observed in either a swimming motility defective fliL mutant or an arsenite oxidase defective aoxB mutant; both strains displayed the wild-type surface properties and growth capacities. We propose that during the biofilm formation process arsenite acts on swimming motility as a result of the arsenite oxidase activity, preventing the switch between planktonic and sessile lifestyles. Our study therefore highlights the existence, under arsenite exposure, of a competition between swimming motility, resulting from arsenite oxidation, and biofilm initiation.

Collimonas fungivorans, an unpredicted in vitro but efficient in vivo biocontrol agent for the suppression of tomato foot and root rot

Although bacteria from the genus Collimonas have demonstrated in vitro antifungal activity against many different fungi, they appeared inactive against the plant-pathogenic fungus Fusarium oxysporum f.sp. radicis-lycopersici (Forl), the causal agent of tomato foot and root rot (TFRR). Visualization studies using fluorescently labelled organisms showed that bacterial cells attached extensively to the fungal hyphae under nutrient-poor conditions but not in glucose-rich Armstrong medium. Collimonas fungivorans was shown to be as efficient in colonizing tomato root tips as the excellent colonizer Pseudomonas fluorescens strain WCS365. Furthermore, it appeared to colonize the same sites on the root as did the phytopathogenic fungus. Under greenhouse conditions in potting soil, C. fungivorans performed as well in biocontrol of TFRR as the well-established biocontrol strains P. fluorescens WCS365 and Pseudomonas chlororaphis PCL1391. Moreover, under biocontrol conditions, C. fungivorans did not attach to Forl hyphae colonizing plant roots. Based on these observations, we hypothesize that C. fungivorans mainly controls TFRR through a mechanism of competition for nutrients and niches rather than through its reported mycophagous properties, for which attachment of the bacteria to the fungal hyphae is assumed to be important.

Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium

An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genusHerminiimonasof the familyOxalobacteraceae, orderBurkholderialesin theBetaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1TandHerminiimonas fonticolaS-94Tand between strain ULPAs1TandHerminiimonas aquatilisCCUG 36956Trevealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1T(=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species ofHerminiimonas, for which the nameHerminiimonas arsenicoxydanssp. nov. is proposed.

Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China

Four Gram-negative, motile, rod-shaped bacterial strains were isolated from soil samples collected from south-east China. A taxonomic study including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics was performed. DNA G+C contents of the four strains were 63-66 mol%. Their predominant ubiquinone was Q-8. The fatty acid profiles contained C16:1omega7c (36.9-54.7%) and C16:0 (22.8-25.5%) as the major components. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and DNA-DNA hybridization results, the four isolates are considered to represent four novel species of the genus Massilia, for which the names Massilia dura sp. nov. (type strain 16T=CCTCC AB 204070T=KCTC 12342T), Massilia albidiflava sp. nov. (type strain 45T=CCTCC AB 204071T=KCTC 12343T), Massilia plicata sp. nov. (type strain 76T=CCTCC AB 204072T=KCTC 12344T) and Massilia lutea sp. nov. (type strain 101T=CCTCC AB 204073T=KCTC 12345T) are proposed.

Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China

A taxonomic study was performed on strain YIM 31775(T), which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 degrees C and 6.5 to 12.0, respectively; the optimum growth temperature and pH were 28-37 degrees C and 7.0-9.0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C(16 : 1)omega7c (42.4 %) and C(16 : 0) (28.1 %). The DNA G + C content was 62.4 +/ -0.3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775(T) should be placed within the family 'Oxalobacteraceae', in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775(T) should be classified as representing a novel member of the family 'Oxalobacteraceae', for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775(T) (= CCTCC AA 204003(T) = KCTC 12194(T)).

Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water

Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov.

Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil

A mesophilic bacterium, designated strain YIM 31327T, was isolated from a forest soil sample collected from Yunnan Province, China, and was then investigated using a polyphasic approach. The strain grew optimally at 28-30 degrees C and pH 7.2. The cells were Gram-negative, short, rod-shaped, motile and non-spore-forming with flagella. The major ubiquinone was Q-8 and the cellular fatty acids were C(16 : 0) and C(12 : 0). The DNA G + C content of strain YIM 31327T was 62.8 mol%. Phylogenetic analysis revealed that strain YIM 31327T was a member of the beta-Proteobacteria, being most closely related to Duganella zoogloeoides, with which it exhibited less than 96 % 16S rRNA gene sequence similarity. On the basis of the phenotypic and genotypic differences between strain YIM 31327T and D. zoogloeoides, a novel species, Duganella violaceinigra sp. nov., is proposed, with YIM 31327T (= CIP 108077T = KCTC 12193T) as the type strain.