Isolation of soybean-specific plant growth-promoting rhizobacteria using soybean agglutin and evaluation of their effects to improve soybean growth, yield, and soil nutritional status

The basic requirements of plant growth-promoting rhizobacteria (PGPR) for field applications are that they have an affinity for the host plant and that they can colonize the rhizosphere. Here, a new technique was established using soybean agglutin (SBA) as a tool to isolate soybean-specific PGPR. Thirty-three PGPR strains with an affinity for soybean were obtained via the screening method with SBA. All 33 isolates were able to produce indole acetic acid and solubilize inorganic phosphate and potassium. Most isolates (93.94%) were able to solubilize organic phosphate and almost half (45.45%) were able to produce siderophores. More than 40% of the isolates exhibited all five plant growth-promoting traits. The isolate Enterobacter sp. strain DN9 was selected for further analyses of its rhizosphere colonization and soybean growth-promoting effects because of its excellent activity in phosphate and potassium solubilization. The luciferase luxAB gene was electrotransformed into DN9, and the labelled DN9 (DN9-L) was able to survive in the soybean rhizosphere and colonize new spaces as the soybean roots elongated. This strain positively affected root system development and soybean seedling growth. In pot and field experiments, the isolates DN9, DW1, and DW13 significantly increased the nutrient contents in rhizosphere soil and soybean leaves. On average, the seed number per plant and the seed weight per plant were increased by 20% and 24% respectively, in plants inoculated with these PGPR strains in the pot experiment. In a field experiment, compared with uninoculated plants, those inoculated with DW1 showed 46.78% higher pod number per plant and 5.23% higher seed oil content; those inoculated with DW13 showed 79.82% higher seed number per plant and 65.10% higher seed weight per plant; and those inoculated with DN9 showed 9.13% higher 100-seed weight. These results show that SBA can be used as a tool to isolate efficient PGPR to enhance soybean production.

Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity

Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in α-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review

Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria's structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.

Temporal compositional shifts in an activated sludge microbiome during estrone biodegradation

Microbial biodegradation is a key process for the removal of estrogens during wastewater treatment. At least four degradation pathways for natural estrogens have been proposed. However, major estrogen degraders and the occurrence of different estrogen biodegradation pathways in wastewater treatment plants have been rarely investigated. This study was conducted to elucidate estrone biodegradation pathway and to identify key estrone-degrading bacteria in activated sludge from a major wastewater treatment plant in Bahrain. The biodegradation experiments were performed in activated sludge microcosms supplemented with estrone. Sludge samples were retrieved at time intervals to analyze the biodegradation metabolites and the temporal shifts in the bacterial community composition. Chemical analysis revealed the biodegradation of more than 90% of the added estrone within 6 days, and the compounds 4-hydroxyestrone and pyridinestrone acid, which are typical markers of the 4,5-seco pathway of aerobic estrone biodegradation, were detected. Temporal shifts in the relative abundance of bacteria were most prominent among members of Proteobacteria and Bacteroidetes. While the alphaproteobacterial genera Novosphingobium and Sphingoaurantiacus were significantly enriched (from ≤ 6% to an average of 31%) in the estrone-amended activated sludge after 2 days of incubation, the bacteroidete Pedobacter was uniquely detected in these microcosms at day 10. The relative abundance of Polyangia (Nannocyctis) increased to an average of 10 ± 0.4% in the estrone-amended activated sludge after 4 days of incubation. Enrichment cultivation of bacteria from the activated sludge on estrone resulted in a mixed culture that was capable of degrading estrone. An estrone-degrading strain was isolated from this mixed culture and was affiliated with the known estrogen-degrading Alphaproteobacteria Sphingobium estrogenivorans. We conclude that estrone degradation in the activated sludge from the studied wastewater treatment plant proceeds via the 4,5-seco pathway and is most likely mediated by alphaproteobacterial taxa.

Genome Resource of Ancylobacter pratisalsi E130T: A Novel Plant-Growth-Promoting Bacterium Isolated from the Rhizosphere

Ancylobacter pratisalsi sp. nov. strain E130^T is a Gram-negative, nonmotile, aerobic, and rod-shaped bacterium that was recently isolated from the rhizosphere of Plantago winteri Wirtg. from a natural salt meadow. This strain was described as novel species in genus Ancylobacter; however, information about its complete genome has yet not been reported. In this study, its genome was completely sequenced by PacBio SMRT cell platform, analyzed, and compared with other selected complete genome sequences of Ancylobacter to elucidate its potential plant growth promotion abilities. The genomic analysis revealed that the genome of strain E130^T consists of one circular DNA chromosome of 4,618,530 bp with a GC content of 66% and one plasmid of 159,741 bp with a GC content of 64.13%. The entire genome contains 4,322 predicted coding genes, 49 transfer RNAs, and 6 ribosomal RNA genes. Genome analysis identified a siderophore natural product biosynthesis cluster, which produces fuscachelin. Knockout of several key genes in this cluster significantly reduces the plant-growth-promotion ability of the strain E130^T. In addition to plant-growth promotion, the strain E130^T can grow well on 5% NaCl (wt/vol), indicating that this strain is a potential bioresource for successful production of economic crops in alkaline soil.

Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria

Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.

Acesulfame aerobic biodegradation by enriched consortia and Chelatococcus spp.: Kinetics, transformation products, and genomic characterization

The artificial sweetener Acesulfame (ACE) has been frequently detected in wastewater treatment plants (WWTPs) and is regarded as an emerging pollutant due to its low biodegradability. However, recent observations of ACE biodegradation in WWTPs have stimulated interest in the ACE-degrading bacteria and mineralization pathways. In this study, next-generation sequencing methods, Illumina and Nanopore sequencing, were combined to explore the ACE-degrading communities enriched from the activated sludge of six municipal wastewater treatment plants. Metagenomic investigations indicated that all enrichments were similarly dominated by the phyla Proteobacteria and Planctomycetes. Notably, at the species level, four metagenome-assembled genomes (MAGs) were shared by six enriched communities with considerable abundances, indicating that they may be responsible for ACE biodegradation in the enrichments. Besides, two ACE-degrading pure strains, affiliated to the genus Chelatococcus, were isolated from the enrichment. The genomic analysis showed that these two isolates were the new species that were genetically distinct from their relatives. Two type strains, Chelatococcus asaccharovorans DSM 6462 and Chelatococcus composti DSM 101465, could not degrade ACE, implying that the ACE-degrading capability was not shared among the different species in the genus Chelatococcus. The results of the degradation experiment showed that the two isolates could use ACE as the sole carbon source and mineralize ~90% of the total organic carbon. Three biotransformation products (TP96, TP180B, and TP182B) were demonstrated by UPLC-QTOF-MS. The results of this study provide valuable insights into ACE biodegradation and its biotransformation products.

Insights from comparative proteomic analysis into degradation of phenanthrene and salt tolerance by the halophilic Martelella strain AD-3

A halophilic PAHs-degrading strain, Martelella AD-3, was previously isolated from highly saline petroleum-contaminated soil. In this study, label-free proteomics were performed to identify differentially expressed proteins (DEPs) under Group P (phenanthrene +5% salinity) and Group G (glycerol +1% salinity), which would help to reveal the mechanism of phenanthrene degradation and salt tolerance. A total of 307 up-regulated DEPs were found in Group P, including 17 phenanthrene degradation proteins. Among these phenanthrene-degrading proteins, the ferredoxin of aromatic ring-hydroxylating dioxygenase (RHD) was up-regulated by 110-fold and gentisate 1,2-dioxygenases (GDOs) were only expressed in Group P. Besides, we also found nine high salt stress response proteins, including ectoine synthase and transport protein of compatible (osmoprotectant) solutes, were differentially up-regulated. These results indicate that strain AD-3 mainly relied on RHD and dihydrodiol dehydrogenase to degrade phenanthrene, and accumulated compatible solutes for resistance to salt stress. This study provides strong theoretical guidance for understanding the degradation of phenanthrene by strain AD-3 in high salt environments.

Bacterial diversity in ballast water and sediments revealed by 2b-RAD sequencing

Despite that the ballast water management (BWM) convention has come into force to prevent the spread of harmful aquatic organisms, to date, very few bacteria can be identified through microbial culture method. In this study, we explored a reduced-representation sequencing of 2b-RAD approach to investigate the bacterial diversity in ballast water and sediments (BWS). Our results indicated a large amount of bacteria species (1496) detected in BWS up to now, including 13 pathogens that are seriously concerning in marine environment and aquaculture like the most harmful Vibrio harveyi and Aurantimonas coralicida. We showed that the ballast water had relative lower species, which was dominated by Proteobacteria. In contrast, the sediments had richer species, which was dominated by Bacteroidetes. Although BWS differed significantly in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management. In conclusion, 2b-RAD sequencing shows promise in future BWM.

Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems

Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by which B. saltans becomes addicted to its endosymbiont. Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts of Paracaedibacter-like bacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.

nov.: members of Alphaproteobacteria isolated from sea sand

Two Gram-negative, rod bacteria, strains DP07^T and DP05^T, showing catalase- and oxidase-positive activities, were isolated from sea sand in South Korea. Strain DP07^T was strictly aerobic and had a yellow colony colour. Contrastingly, strain DP05^T was facultatively aerobic and had a creamy colony colour. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain DP07^T contained cyclo-C_19:0 ω8c, C_16:0, summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c), and C_16:0 2-OH as the major fatty acids and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, and an unidentified polar lipid as the major polar lipids. Strain DP05^T contained C_16:0, cyclo-C_19:0, and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c) as the major fatty acids and phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, and two unidentified polar lipids as the major polar lipids. Cadaverine was detected as the predominant polyamine in both strains. The DNA G + C contents of strains DP07^T and DP05^T were 66.1 mol% and 51.8 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains DP07^T and DP05^T formed close phylogenetic lineages with Maritimibacter alkaliphilus HTCC2654^T (similarity, 98.1%) and Sneathiella chungangensis CAU 1294 ^T (similarity, 98.5%), respectively. The average nucleotide identity and DNA-DNA hybridisation values between strain DP07^T and M. alkaliphilus were 80.0% and 23.0%, respectively, and those between strain DP05^T and S. chungangensis were 77.1% and 19.9%, respectively. Based on the results of phenotypic, chemotaxonomic, and molecular analyses, strains DP07^T and DP05^T represent two novel species of the genera Maritimibacter and Sneathiella, respectively, for which we propose the following names: Maritimibacter harenae sp. nov. and Sneathiella litorea sp. nov. The type strains of M. harenae and S. litorea were DP07^T (= KACC 21429 ^T = JCM 33811 ^T) and DP05^T (= KACC 21431 ^T = JCM 33810 ^T), respectively.

Biogenic fenton-like reaction involvement in aerobic degradation of C60 by Labrys sp. WJW

Buckminster fullerene (C₆₀), the most representative type among fullerenes, has attracted widely attentions because of its many potential applications. The increasing application of fullerene and limited knowledge of its environmental fate are required concerns. Herein, the biotransformation of C₆₀ by Labrys sp. WJW was investigated. Cell numbers reached 25.76 ± 1.85 folds within 8 days using 100 mg/L C₆₀ as sole carbon source. The biotransformation of C₆₀ by Labrys sp. WJW was analyzed by various characterization methods. Raman spectra indicated that strain WJW broke the soccer ball like structure of C₆₀. After 12 days, over 60% of C₆₀ was degraded evidenced by UV-vis spectrophotometry and liquid chromatography-mass spectrometry. The underlying biotransformation mechanism of C₆₀ through an extracellular Fenton-like reaction was illustrated. In this reaction, the ^•OH production was mediated by reduction of H₂O₂ involving a continuous cycle of Fe(II)/Fe(III). Bacterial transformation of C₆₀ will provide new insights into the understanding of C₆₀ bioremediation process.

Spatial distribution and functional profile of the bacterial community in response to eutrophication in the subtropical Beibu Gulf, China

In this study, we investigated the specific bacterial distribution and the response of bacterial communities to shifts in environmental factors in the subtropical Beibu Gulf, southern China. The abundances of Actinobacteria, Bacilli, Planctomycetia, Thermoleophilia, Anaerolineae, and Synechococcophycideae were significantly higher in high eutrophic samples than in medium eutrophic and oligotrophic samples. Bacterial alpha-diversity was found greater in high eutrophication samples than in the other samples. Besides, Ponticaulis koreensis, Nautella italic, Anaerospora hongkongensis, Candidatus Aquiluna rubra, and Roseovarius pacificus were sensitive to trophic variation and thus could be used as eco-markers. In addition, the relative abundances of functional genes involving carbohydrate and amino acid metabolism were very high among the samples. We also found temperature, Chl-a, TDN and NO₃^- were the main environmental drivers of bacterial community structure. Overall, this study provides new insight into the composition of bacterial community and function response to gradients of eutrophication in Beibu Gulf.

Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation

Variability in the apparent CO₂ fixation yield of four aerobic sulfur-oxidizing bacteria (Halothiobacillus neapolitanus DSM 15147, Thiobacillus thioparus DSM 505, Thiomonas intermedia DSM 18155, and Starkeya novella DSM 506) in autotrophic culturing was studied, and mutual effects of key intrinsic factors on CO₂ fixation were explored. DSM 15147 and DSM 505 exhibited much higher CO₂ fixation yields than DSM 18155 and DSM 506. The differences in CO₂ fixation yield were determined not only by cbb gene transcription, but also by cell synthesis rate, which was determined by rRNA gene copy number; the rRNA gene copy number had a more significant effect than cbb gene transcription on the apparent CO₂ fixation yield. Moreover, accumulation of EDOC was observed in all four strains during chemoautotrophic cultivation, and the proportion of EDOC accounting for total fixed organic carbon (TOC; EDOC/TOC ratio) was much higher in DSM 18155 and DSM 506 than in DSM 15147 and DSM 505. The accumulation of EDOC led to a significant decrease in the cbb gene transcription efficiency during cultivation, and a further feedback inhibitory effect on CO₂ fixation.

Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria

Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.

Biodegradation aspects of ibuprofen and identification of ibuprofen-degrading microbiota in an immobilized cell bioreactor

An enrichment process was employed by applying high ibuprofen concentration in an immobilized cell bioreactor in order to favor the ibuprofen-degrading community present in activated sludge. Experimental data showed the ability of the immobilized cell bioreactor to achieve high ibuprofen removal efficiencies (98.4 ± 0.3%), the tendency of the enriched biomass to acidify the treated liquor, and the inhibition of the nitrification process. Illumina sequencing revealed a massive increase in the relative abundance of Alphaproteobacteria and Gammaproteobacteria (from 29.1 to 80.8%) and a dramatic decrease in the proportion of Bacteroidetes, Planctomycetes, and Verrucomicrobia (from 42.7 to 2.1%) when pure ibuprofen served as the sole carbonaceous feeding substrate. This shift in the feeding conditions resulted in the predominance of Novosphingobium and Rhodanobacter (25.5 ± 10.8% and 25.2 ± 3.0%, respectively) and demonstrated a specialized ibuprofen-degrading bacterial community in activated sludge, which possessed the selective advantage to cope with its degradation. To the best of our knowledge, this bioreactor system was capable of effectively treating the highest ibuprofen concentration applied in wastewater treatment plants.

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure

Micropollutants of emerging concern such as pharmaceuticals can significantly affect the performance of secondary biological processes in wastewater treatment plants. The present study is aimed to evaluate the toxicity and inhibition of three pharmaceutical compounds (caffeine, sulfamethoxazole and carbamazepine) on two cultures of microbial consortia enriched from wastewater aerobic activated sludge. One of them was acclimated to pharmaceuticals and the other was non-acclimated as control bioassay. The toxic and inhibitory effects on these cultures were assessed by respirometric tests through the oxygen uptake rate as an indicator of their capacity to degrade a readily available carbon source. Higher values of toxicity and inhibition of pharmaceutical compounds were observed for the control culture as compared to the acclimated one. Sulfamethoxazole and carbamazepine exhibited higher toxicity and inhibition effects than caffeine in both acclimated and control cultures. The microbial diversity of the two cultures was also studied. The composition of microbial community of acclimated and control cultures, was determined by targeting the 16S ribosomal RNA gene. It was observed that Proteobacteria was the most abundant phylum, with Gammaproteobacteria dominating both cultures. Control culture was dominated by Gammaproteobacteria and mostly by the genera Pseudomonas and Sodalis, which belong to common families present in wastewater. Results suggested that the acclimated culture to the three pharmaceuticals was mostly comprised of the extremely multiresistant genera Escherichia-Shigella (38%) of Gammaproteobacteria, resulting to higher resistance as compared to the control culture (Escherichia-Shigella, 7%). Finally, the microbial structure of the microorganisms present in a real bioreactor, which was initially seeded with the acclimated culture and fed in a continuous mode with the selected pharmaceuticals, was also analyzed. The continuous loading of pharmaceuticals in the bioreactor affected its microbial diversity, leading to the dominance of Betaproteobacteria and to the resistant genus Rhizobium of Alphaproteobacteria.

Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants

Although the rhizomicrobiome has been extensively studied, little is known about the interactions between soil properties and the assemblage of plant growth-promoting microbes in the rhizosphere. Herein, we analysed the composition and structure of rhizomicrobiomes associated with soybean and alfalfa plants growing in different soil types using deep Illumina 16S rRNA sequencing. Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizomicrobiome. Plant biomass was influenced by plant species, the composition of the rhizomicrobiome, soil pH, N, P and plant growth stage. The beta diversity of the rhizomicrobiome was the second most influential factor on plant growth (biomass). Rhizomicrobes associated with plant biomass were identified and divided into four groups: (1) positively associated with soybean biomass; (2) negatively associated with soybean biomass; (3) positively associated with alfalfa biomass; and (4) negatively associated with alfalfa biomass. Genera assemblages among the four groups differentially responded to soil properties; Group 1 and Group 2 were significantly correlated with soil pH and P, whereas Group 3 and Group 4 were significantly correlated with soil N, K and C. The influence of soil properties on the relative abundance of plant biomass-associated rhizomicrobes differed between soybean and alfalfa. The results suggest the rhizomicrobiome has a pronounced influence on plant growth, and the rhizomicrobiome assemblage and plant growth-associated microbes are differentially structured by soil properties and leguminous plant species.

Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus

BACKGROUND

Citrus worldwide is threatened by huanglongbing (HLB) and tristeza diseases caused by 'Candidatus Liberibacter asiaticus' (CaLas) and Citrus tristeza virus (CTV). Although the pathogens are members of the α-proteobacteria and Closteroviridae, respectively, both are restricted to phloem cells in infected citrus and are transmitted by insect vectors. The response of sweet orange to single infection by either of these two pathogens has been characterized previously by global gene expression analysis. But because of the ubiquity of these pathogens where the diseases occur, co-infection by both pathogens is very common and could lead to increased disease severity based on synergism. We therefore co-inoculated sweet orange trees with CaLas and either a mild or a severe strain of CTV, and measured changes of gene expression in host plants.

RESULTS

In plants infected with CaLas-B232, the overall alteration in gene expression was much greater in plants co-inoculated with the severe strain of CTV, B6, than when co-infected with the mild strain of CTV, B2. Plants co-infected with CaLas-B232 and either strain of CTV died but trees co-infected with CTV-B2 survived much longer than those co-infected with CTV-B6. Many important pathways were perturbed by both CTV-B2/CaLas-B232 and/or CTV-B6/CaLas-B232, but always more severely by CTV-B6/CaLas-B232. Genes related to cell wall modification and metal transport responded differently to infection by the pathogens in combination than by the same pathogens singly. The expressions of genes encoding phloem proteins and sucrose loading proteins were also differentially altered in response to CTV-B2 or CTV-B6 in combination with CaLas-B232, leading to different phloem environments in plants co-infected by CaLas and mild or severe CTV.

CONCLUSIONS

Many host genes were expressed differently in response to dual infection as compared to single infections with the same pathogens. Interactions of the pathogens within the host may lead to a better or worse result for the host plant. CTV-B6 may exert a synergistic effect with CaLas-B232 in weakening the plant; on the other hand, the responses activated by the mild strain CTV-B2 may provide some beneficial effects against CaLas-B232 by increasing the defense response of the host.

Bacterial Production of a Pederin Analogue by a Free-Living Marine Alphaproteobacterium

The polyketide pederin family are cytotoxic compounds isolated from insects, lichen, and marine sponges. During the past decade, different uncultivable bacteria symbionts have been proposed as the real producers of these compounds, such as those found in insects, lichen, and marine sponges, and their trans-AT polyketide synthase gene clusters have been identified. Herein we report the isolation and biological activities of a new analogue of the pederin family, compound 1, from the culture of a marine heterotrophic alphaproteobacterium, Labrenzia sp. PHM005. This is the first report of the production of a pederin-type compound by a free-living marine bacteria that could be cultured in the laboratory.

Successional trajectories of bacterioplankton community over the complete cycle of a sudden phytoplankton bloom in the Xiangshan Bay, East China Sea

Phytoplankton bloom has imposed ecological concerns worldwide; however, few studies have been focused on the successional trajectories of bacterioplankton community over a complete phytoplankton bloom cycle. Using 16S pyrosequencing, we investigated how the coastal bacterioplankton community compositions (BCCs) respond to a phytoplankton bloom in the Xiangshan Bay, East China Sea. The results showed that BCCs were significantly different among the pre-bloom, bloom, and after-bloom stages, with the lowest bacterial diversity at the bloom phase. The BCCs at the short-term after-bloom phase showed a rapid but incomplete recovery to the pre-bloom phase, evidenced by 69.8% similarity between pre-bloom and after-bloom communities. This recovery was parallel with the dynamics of the operational taxonomic units (OTUs) affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria, whose abundance enriched when bloom occur, and decreased after-bloom, and vice versa. Collectively, the results showed that the BCCs were sensitive to algal-induced disturbances, but could recover to a certain extent after bloom. In addition, OTUs which enriched or decreased during this process are closely associated with this temporal pattern, thus holding the potential to evaluate and indicate the succession stage of phytoplankton bloom.

Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions

Oxygen-depleted hypoxic regions in the tumour are generally resistant to therapies. Although nanocarriers have been used to deliver drugs, the targeting ratios have been very low. Here, we show that the magneto-aerotactic migration behaviour of magnetotactic bacteria, Magnetococcus marinus strain MC-1 (ref. 4), can be used to transport drug-loaded nanoliposomes into hypoxic regions of the tumour. In their natural environment, MC-1 cells, each containing a chain of magnetic iron-oxide nanocrystals, tend to swim along local magnetic field lines and towards low oxygen concentrations based on a two-state aerotactic sensing system. We show that when MC-1 cells bearing covalently bound drug-containing nanoliposomes were injected near the tumour in severe combined immunodeficient beige mice and magnetically guided, up to 55% of MC-1 cells penetrated into hypoxic regions of HCT116 colorectal xenografts. Approximately 70 drug-loaded nanoliposomes were attached to each MC-1 cell. Our results suggest that harnessing swarms of microorganisms exhibiting magneto-aerotactic behaviour can significantly improve the therapeutic index of various nanocarriers in tumour hypoxic regions.

Performance of a new suspended filler biofilter for removal of nitrogen oxides under thermophilic conditions and microbial community analysis

A suspended biofilter, as a new bioreactor, was constructed for the removal of nitrogen oxides (NOX) from simulated flue gas under thermophilic conditions. The suspended biofilter could be quickly started up by inoculating the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1. The NO concentration in the inlet stream ranged from 200mg/m(3) to 2000mg/m(3) during the operation, and inlet loading ranged from 8.2-164g/(m(3)·h). The whole operation period was divided into four phases according to the EBRT. The EBRT of phases I, II, III and IV were 88s (9-43d), 44s (44-61d), 66s (62-79d) and 132s (80-97d), respectively. An average NO removal efficiency of 90% was achieved during the whole operation period, and the elimination capacity increased linearly with the increase in NO inlet loading and the maximum elimination capacity reached 146.9g/(m(3)·h). No clogging was observed, although there was a high biomass concentration in the biofilter bed. The remarkable performance in terms of NO removal could be attributed to the rich bacterial communities. The microbial community structure in the biofilm was investigated by high throughput sequencing analysis (16S rRNA MiSeq sequencing). The experimental results showed that the microbial community structure of the biofilm was very rich in diversity, with the most abundant bacterial class of the Alphaproteobacteria, which accounted for 36.5% of the total bacteria, followed by Gammaproteobacteria (30.7%) and Clostridia (27.5%). It was worthwhile to mention that the dominant species in the suspended biofilter biofilm were all common denitrifying bacteria including Rhizobiales (inoculated microbe), Rhodospirillales, Enterobacteriales and Pseudomonadales, which accounted for 19.4%, 17%, 21.6% and 7%, respectively. The inoculated strain TAD1 belonged to Alphaproteobacteria class. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, 16S rRNA gene sequencing of these bacteria could provide more functional and phylogenetic information about the bacterial communities.

Digital Gene Expression Analysis of Ponkan Mandarin (Citrus reticulata Blanco) in Response to Asia Citrus Psyllid-Vectored Huanglongbing Infection

Citrus Huanglongbing (HLB), the most destructive citrus disease, can be transmitted by psyllids and diseased budwoods. Although the final symptoms of the two main HLB transmission ways were similar and hard to distinguish, the host responses might be different. In this study, the global gene changes in leaves of ponkan (Citrus reticulata) mandarin trees following psyllid-transmission of HLB were analyzed at the early symptomatic stage (13 weeks post inoculation, wpi) and late symptomatic stage (26 wpi) using digital gene expression (DGE) profiling. At 13 wpi, 2452 genes were downregulated while only 604 genes were upregulated in HLB infected ponkan leaves but no pathway enrichment was identified. Gene function analysis showed impairment in defense at the early stage of infection. At late stage of 26 wpi, however, differentially expressed genes (DEGs) involved in carbohydrate metabolism, plant defense, hormone signaling, secondary metabolism, transcription regulation were overwhelmingly upregulated, indicating that the defense reactions were eventually activated. The results indicated that HLB bacterial infection significantly influenced ponkan gene expression, and a delayed response of the host to the fast growing bacteria might be responsible for its failure in fighting against the bacteria.

Input of organic matter enhances degradation of weathered diesel fuel in sub-tropical sediments

We investigated different types of biostimulation practices to enhance degradation of weathered conventional diesel fuel in sandy beach sediments from coastal Alabama. Biodegradation rates were measured following the addition of either inorganic nutrients, or organic matter derived from either plant material (Spartina alterniflora) or fish tissue (Chloroscombrus chrysurus) both common to the region. The greatest hydrocarbon degradation rates were observed in the C. chrysurus amended treatments (k=0.0119 d(-1)). Treatment with fish-derived organic matter increased the degradation rates by 104% as compared to control treatments, while inorganic nutrient addition increased the degradation rates by 57%. The addition of plant derived organic matter, however, only marginally enhanced the degradation rates (~7%) during the course of the study. Bacterial 16S rRNA analyses revealed that most sediment microorganisms belonged to the classes; Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The most frequently abundant hydrocarbon degraders were mostly similar to Achromobater sp., Microbulbifer sp., Ruegeria sp., and Pseudomonas sp.

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral

Bacterial diseases affecting scleractinian corals pose an enormous threat to the health of coral reefs, yet we still have a limited understanding of the bacteria associated with coral diseases. White band disease is a bacterial disease that affects the two Caribbean acroporid corals, the staghorn coral Acropora cervicornis and the elkhorn coral A. palmate. Species of Vibrio and Rickettsia have both been identified as putative WBD pathogens. Here we used Illumina 16S rRNA gene sequencing to profile the bacterial communities associated with healthy and diseased A. cervicornis collected from four field sites during two different years. We also exposed corals in tanks to diseased and healthy (control) homogenates to reduce some of the natural variation of field-collected coral bacterial communities. Using a combination of multivariate analyses, we identified community-level changes between diseased and healthy corals in both the field-collected and tank-exposed datasets. We then identified changes in the abundances of individual operational taxonomic units (OTUs) between diseased and healthy corals. By comparing the diseased and healthy-associated bacteria in field-collected and tank-exposed corals, we were able to identify 16 healthy-associated OTUs and 106 consistently disease-associated OTUs, which are good candidates for putative WBD pathogens. A large percentage of these disease-associated OTUs belonged to the order Flavobacteriales. In addition, two of the putative pathogens identified here belong to orders previously suggested as WBD pathogens: Vibronales and Rickettsiales.

[Petroleum pollution and the microbial community structure in the soil of Shengli Oilfield]

Soils around a new oil well (2011- ) and an old oil well (1966-2003) were sampled to investigate the characteristics of petroleum pollution in the oilfield. The structure of soil microbial community was analyzed by PCR-DGGE and clone sequencing techniques. Results showed that the soils around the two oil wells were generally contaminated with petroleum, and the concentrations of total petroleum hydrocarbons mostly exceeded the threshold of the environmental quality standards of soil (500 mg x kg(-1)). The total petroleum hydrocarbons concentration of the polluted soil was significantly positively correlated with the contents of organic carbon, total nitrogen and available potassium, respectively. The microbial diversity index in the soil around the old oil well decreased with the increasing total petroleum hydrocarbons concentration, however, it was reversed for the soil around the new oil well. Sequence analysis of the prominent bands in DGGE profiles showed that some dominant species existed in the petroleum-contaminated soils around the oil wells and mostly were oil-associated and hydrocarbon degrading bacteria, including Microbacterium, Streptomyces, Dietzia, Flavobacterium, alpha-Proteobacteria, and gamma-Proteobacteria.

Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont

The genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. Recoding of UGA from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. Small genomes typically exhibit low guanine plus cytosine (GC) content, and this bias in base composition has been proposed to drive UGA Stop to Tryptophan (Stop→Trp) recoding. Using a combination of genome sequencing and high-throughput proteomics, we show that an α-Proteobacterial symbiont of cicadas has the unprecedented combination of an extremely small genome (144 kb), a GC–biased base composition (58.4%), and a coding reassignment of UGA Stop→Trp. Although it is not clear why this tiny genome lacks the low GC content typical of other small bacterial genomes, these observations support a role of genome reduction rather than base composition as a driver of codon reassignment.

The genetic code, which relates DNA sequence to protein sequence, is nearly universal across all life. Examples of recodings do exist, but new instances are rare. Genomes that exhibit recodings typically have other extreme properties, including reduced size, reduced gene sets, and low guanine plus cytosine (GC) content. The most common recoding event, the reassignment of UGA to Tryptophan instead of Stop (Stop→Trp), was previously known from several mitochondrial and one bacterial lineage, and it was proposed to be driven by extinction of the UGA codon due to reduction in GC content. Here we present an unusual bacterial genome from a symbiont of cicadas. It exhibits the UGA Stop→Trp reassignment, but has a high GC content, showing that reduction in GC content is not a necessary condition for this recoding. This symbiont genome is also the smallest known for any cellular organism. We therefore propose gene loss during genome reduction as the common force driving this code change in bacteria and organelles. Additionally, the extremely small size of the genome further obscures the once-clear distinction between organelle and autonomous bacterial life.

The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria

The phylogenetic diversity of prokaryotic communities exposed to arid conditions in the hot desert of Tataouine (south Tunisia) was estimated with a combination of a culture and - molecular-based analysis. Thirty-one isolates, representative of each dominant morphotypes, were affiliated to Actinobacteria, Firmicutes, Proteobacteria and the CFB group while none related to Archaea. Analysis of 16S rRNA gene libraries revealed the presence of species related to Bacteria and Archaea. Sequences related to Archaea were all affiliated to the non-thermophilic Crenarchaeota subgroup. Bacterial sequences were dominated by Proteobacteria, Actinobacteria and Acidobacteria; a few sequences were distributed among eight others phyla, including Thermus/Deinococcus relatives. A correlation between tolerance to desiccation and to radiation has been demonstrated for the radiotolerant bacteria Deinococcus radiodurans. Because bacteria living in the hot desert of Tataouine are one way or another tolerant to desiccation, we investigate whether they could also be tolerant to radiation. Exposition of soil samples to intense gamma radiation yields Bacillus, Thermus/Deinococcus and alpha-Proteobacteria relatives. Four of these strains correspond to radiotolerant species as revealed by evaluation of the resistance levels of the individual cultures. A detailed analysis of the resistance levels for two Thermus/Deinococcus and two alpha-Proteobacteria relatives revealed that they correspond to new radiotolerant species.

Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle

Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, some of which also take part in the extraction of metal ions from their sulfur containing ores. These sulfur oxidizers oxidize inorganic sulfur compounds like sulfide, thiosulfate etc. to produce reductants that are used for carbon dioxide fixation or in respiratory electron transfer chains. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxV is known to be a CcdA homolog involved in the transport of reductants from cytoplasm to periplasm. SoxW and SoxS are periplasmic thioredoxins, which (SoxW) interact with SoxV and thereby help in the redox reactions. We have employed homology modeling to construct the three-dimensional structures of the SoxV, SoxW and SoxS proteins from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics simulations we have identified the amino acid residues of these proteins involved in the interaction. The probable biochemical mechanism of the transport of reductants through the interactions of these proteins has also been investigated. Our study provides a rational basis to interpret the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.

Plasticity of a transcriptional regulation network among alpha-proteobacteria is supported by the identification of CtrA targets in Brucella abortus

CtrA is a master response regulator found in many alpha-proteobacteria. In Caulobacter crescentus and Sinorhizobium meliloti, this regulator is essential for viability and is transcriptionally autoregulated. In C. crescentus, it is required for the regulation of multiple cell cycle events, such as DNA methylation, DNA replication, flagella and pili biogenesis and septation. Here, we report the characterization of the ctrA gene homologue in the alpha2-proteobacteria Brucella abortus, a facultative intracellular pathogen responsible for brucellosis. We detected CtrA expression in the main Brucella species, and its overproduction led to a phenotype typical of cell division defect, consistent with its expected role. A purified B. abortus CtrA recombinant protein (His6-CtrA) was shown to protect the B. abortus ctrA promoter from DNase I digestion, suggesting transcriptional autoregulation, and this protection was enhanced under CtrA phosphorylation on a conserved Asp residue. Despite the similarities shared by B. abortus and C. crescentus ctrA, the pathway downstream from CtrA may be distinct, at least partially, in both bacteria. Indeed, beside ctrA itself, only one (the ccrM gene) out of four B. abortus homologues of known C. crescentus CtrA targets is bound in vitro by phosphorylated B. abortus CtrA. Moreover, further footprinting experiments support the hypothesis that, in B. abortus, CtrA might directly regulate the expression of the rpoD, pleC, minC and ftsE homologues. Taken together, these results suggest that, in B. abortus and C. crescentus, similar cellular processes are regulated by CtrA through the control of distinct target genes. The plasticity of the regulation network involving CtrA in these two bacteria may be related to their distinct lifestyles.

Origins of hydrogenosomes and mitochondria

Complete genome sequences for many oxygen-respiring mitochondria, as well as for some bacteria, leave no doubt that mitochondria are descendants of alpha-proteobacteria, a finding for which the endosymbiont hypothesis can easily account. Yet a wealth of data indicate that mitochondria and hydrogenosomes - the ATP-producing organelles of many anaerobic protists - share a common ancestry, a finding that traditional formulations of the endosymbiont hypothesis less readily accommodates. Available evidence suggests that a more in-depth understanding of the origins of eukaryotes and their organelles will hinge upon data from the genomes of protists that synthesize ATP without the need for oxygen.

Optimum treatment of intracellular infection

The intracellular location of some micro-organisms has been early recognised as a critical point to explain failure of antibiotic therapy to eradicate such pathogens from infected hosts. Most often parasites invade 'professional' phagocytic cells, including neutrophils, monocytes and macrophages, by resisting the intracellular bactericidal phagolysosomal pathway. Alternatively, they may invade 'non-professional' phagocytic cells (cells with fewer phagocytic and bactericidal abilities) such as endothelial cells, or even cells without lysosomes such as erythrocytes. The intracellular activity of an antibiotic depends on several factors including its ability to reach the eukaryotic cell membrane, its subcellular localisation as compared to that of the parasite, the possibility that the intracellular milieu may partially inactivate its activity, and the susceptibility of the intracellular form of the parasite. In vitro and animal models have been developed to investigate antibiotic activity against intracellular pathogens. However, it should be emphasised that only data obtained from patients give reliable information to define the optimum antibiotic regimen.

Comments on the classification of the order Rickettsiales

The classification of the Rickettsiales is discussed for taxa above species. A new Class, Microtatobiotes, meaning smallest life, is proposed to include Orders Rickettsiales and Virales. Other new proposals are: Tribe Wolbachiae under Rickettsiales including two new genera Symbiotes (genotype Rickettsia lectularia Arkwright et al.) and Rickettsiella (genotype Coxiella popillae Dutky and Gooden). Extensive new synonymy is provided in genera and species under Rickettsia, Coxiella, Cowdria, Miyagawanella, and Wolbachia.