Bacterial communities of three plant species from Pb-Zn contaminated sites and plant-growth promotional benefits of endophytic Microbacterium sp. (strain BXGe71)

Spatial and temporal dynamics of microbes and genes in drinking water reservoirs: Distribution and potential for taste and odor generation

Numerous reservoirs encounter challenges related to taste and odor issues, often attributed to odorous compounds such as geosmin (GSM) and 2-methylisoborneol (2-MIB). In this study, two large reservoirs located in northern and southern China were investigated. The Jinpen (JP) reservoir had 45.99 % Actinomycetes and 14.82 % Cyanobacteria, while the Xikeng (XK) reservoir contained 37.55 % Actinomycetes and 48.27 % Cyanobacteria. Most of the 2-MIB produced in surface layers of the two reservoirs in summer originated from Cyanobacteria, most of the 2-MIB produced in winter and in the bottom water originated from Actinomycetes. Mic gene abundance in the XK reservoir reached 5.42 × 104 copies/L in winter. The abundance of GSM synthase was notably high in the bottom layer and sediment of both reservoirs, while 2-MIB synthase was abundant in the surface layer of the XK reservoir, echoing the patterns observed in mic gene abundance. The abundance of odor-producing enzymes in the two reservoirs was inhibited by total nitrogen, temperature significantly influenced Actinomycetes abundance in the JP reservoir, whereas dissolved oxygen had a greater impact in the XK reservoir. Overall, this study elucidates the molecular mechanisms underlying odor compounding, providing essential guidance for water quality management strategies and the improvement of urban water reservoir quality.

An updated view of bacterial endophytes as antimicrobial agents against plant and human pathogens

Bacterial endophytes are a crucial component of the phytomicrobiome, playing an essential role in agriculture and industries. Endophytes are a rich source of bioactive compounds, serving as natural antibiotics that can be effective in combating antibiotic resistance in pathogens. These bacteria interact with host plants through various processes such as quorum sensing, chemotaxis, antibiosis, and enzymatic activity. The current paper focuses on how plants benefit extensively from endophytic bacteria and their symbiotic relationship in which the microbes enhance plant growth, nitrogen fixation, increase nutrient uptake, improve defense mechanisms, and act as antimicrobial agents against pathogens. Moreover, it highlights some of the bioactive compounds produced by endophytes.

Diversity and functional traits of seed endophytes of Dysphania ambrosioides from heavy metal contaminated and non-contaminated areas

Seed endophytes played a crucial role on host plants stress tolerance and heavy metal (HM) accumulation. Dysphania ambrosioides is a hyperaccumulator and showed strong tolerance and extraordinary accumulation capacities of multiple HMs. However, little is known about its seed endophytes response to field HM-contamination, and its role on host plants HM tolerance and accumulation. In this study, the seed endophytic community of D. ambrosioides from HM-contaminated area (H) and non-contaminated area (N) were investigated by both culture-dependent and independent methods. Moreover, Cd tolerance and the plant growth promoting (PGP) traits of dominant endophytes from site H and N were evaluated. The results showed that in both studies, HM-contamination reduced the diversity and richness of endophytic community and changed the most dominant endophyte, but increased resistant species abundance. By functional trait assessments, a great number of dominant endophytes displayed multiple PGP traits and Cd tolerance. Interestingly, soil HM-contamination significantly increased the percentage of Cd tolerance isolates of Agrobacterium and Epicoccum, but significantly decreased the ration of Agrobacterium with the siderophore production ability. However, the other PGP traits of isolates from site H and N showed no significant difference. Therefore, it was suggested that D. ambrosioides might improve its HM tolerance and accumulation through harboring more HM-resistant endophytes rather than PGP endophytes, but to prove this, more work need to be conducted in the future.

Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area

This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L-1), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L-1), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg-1·h-1), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.

Auxin production and plant growth promotion by Microbacterium albopurpureum sp. nov. from the rhizoplane of leafless Chiloschista parishii Seidenf. orchid

The strains of the genus Microbacterium, with more than 150 species, inhabit diverse environments; plant-associated bacteria reveal their plant growth-promoting activities due to a number of beneficial characteristics. Through the performance of diverse techniques and methods, including isolation of a novel Microbacterium strain from the aerial roots of leafless epiphytic orchid, Chiloschista parishii Seidenf., its morphological and biochemical characterization, chemotaxonomy, phylogenetic and genome analysis, as well as bioassays and estimation of its auxin production capacity, a novel strain of ET2T is described. Despite that it shared 16S rRNA gene sequence similarity of 99.79% with Microbacterium kunmingense JXJ CY 27-2T, so they formed a monophyletic group on phylogenetic trees, the two strains showed clear divergence of their genome sequences. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values of ET2T differed greatly from phylogenetically close JXJ CY 27-2T. Based on the differences being below the threshold for species similarity, together with the unique chemotaxonomic characteristics, strain ET2T represents a novel species of the genus Microbacterium. Several genes, putatively involved in auxin biosynthesis were predicted. This strain revealed obvious plant growth-promoting activities, including diazotrophy and biosynthesis of tryptophan-dependent auxins (indole-3-acetic and indole-3-pyruvic acids). Microbial auxins directly stimulated the rhizogenesis, so that the ET2T-inoculated seeds of wheat, cucumber and garden cress showed evident promotion in their growth and development, both under optimal and under cold stress conditions. Based on phenotypic, chemotypic and genotypic evidences, the strain ET2T belongs to the genus Microbacterium, order Micrococcales, class Actinomycetes, and it represents a novel species, for which the name Microbacterium albopurpureum sp. nov. is proposed, with strain ET2T (VKPM Ac-2212, VKM Ас-2998) as the type strain.

Complete genome sequence of new Microbacterium sp. strain ET2, isolated from roots of leafless orchid

Whole-genome sequence of ET2 strain, isolated from the roots of leafless orchid, constitutes a single circular chromosome of 3,604,840 bp (69.44% G + C content). BLAST+-based average nucleotide identity (ANIb) and digital DNA-DNA hybridization values indicate that ET2 may be a novel Microbacterium species. Genes putatively involved in plant-microbial interactions were predicted.

Trends in phytoremediation of heavy metals-contaminated soils: A Web of science and CiteSpace bibliometric analysis

Heavy metals pollution in soils is an urgent environmental issue worldwide. Phytoremediation is a green and eco-friendly way of remediating heavy metals. However, a systematic overview of this field is limited, and little is known about future development trends. Therefore, we used CiteSpace software to conduct bibliometric and visual analyses of published literature in the field of phytoremediation of heavy metals in soils from the Web of Science core collection and identified research hotspots and development trends in this field. Researchers are paying increased attention to phytoremediation of heavy metals in soils, especially environmental researchers. A total of 121 countries or regions, 3790 institutions, 4091 funded organisations and 15,482 authors have participated in research in this area. China, India, and Pakistan are the largest contributors. There has been extensive cooperation between countries, institutions, and authors worldwide, but there is a lack of cooperation among top authors. 'Calcareous soil', 'Co-contaminated soil' and 'Metal availability' are the most intensively investigated topics. 'EDTA', 'Plant growth-promoting Rhizobacteria', 'Photosynthesis', 'Biochar' and 'Phytoextraction' are research hotspots in this field. In addition, more and more researchers are beginning to pay attention to research on co-contaminated soil, metal availability, chelating agents, and microbial-assisted phytoremediation. In summary, bibliometric, and visual analyses in the field of phytoremediation of heavy metals in soils identifies probable directions for future research and provides a resource through which to better understand this rapidly advancing subject.

Enhanced Cd activation by Coprinus comatus endophyte Bacillus thuringiensis and the molecular mechanism

Fungal endophytes not only tolerate and activate Cd in soil but also promote host growth, yet its Cd activation capacity and mechanism remain unrevealed. Our previous study isolated a robust endophyte Bacillus thuringiensis L1 from Coprinus comatus fruiting body with splendid Cd resistance and activation abilities under laboratory conditions. In this study, those peculiarities were investigated in the actual soil environment. L1 could significantly increase the soil bioavailable Cd content and effectively compensate for alkali-hydro nitrogen losses and microbial inhibition caused by Cd. Furthermore, L1 inoculation improved the soil's bacterial community structure and increased the relative abundance of Cd-resistant bacteria, such as Actinobacteria, Chloroflexi, Acidobacter, and Firmicutes, closely associated with the soil enzyme activity shift. The genome sequencing analysis revealed the presence of genes related to growth promotion, resistance to Cd stress, and Cd activation, which were significantly up-regulated under Cd stress. Notably, L1 mainly activates Cd in soil by secreting citric acid, succinic acid, siderophore, and soluble phosphorus substances to chelate with Cd or dissolve bounded Cd. Meanwhile, the metal-responsive transcription repressor (CadC) and the Cd-translocating protein P-type ATPase (CadA) can help the L1 to suppress the toxicity of Cd. Those results help to unveil the possible mechanism of L1 in Cd-contaminated soil remediation, providing a clear strategy for Cd bio-extraction from soil.

Micro (nano)plastics and phthalate esters drive endophytic bacteria alteration and inhibit wheat root growth

Endophytes play an important role in plant growth and stress tolerance, but limited information is available on the complex effects of micro (nano)plastics and phthalate esters (PAEs) on endophytes in terrestrial plants. To better elucidate the ecological response of endophytic bacteria on exogenous pollutants, a hydroponic experiment was conducted to examine the combined impact of polystyrene (PS) and PAEs on endophyte community structure, diversity, and wheat growth. The findings revealed that wheat roots were capable of absorbing and accumulating PS nanoparticles (PS-NPs, 0.1 μm), whereas PS microparticles (PS-MPs, 1 and 10 μm) merely adhered to the root surface. The addition of PAEs resulted in a stronger accumulation of fluorescent signal from PS-NPs in the roots. The dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) were identified in wheat roots, and they could be metabolized to form minobutyl phthalate and phthalic acid, and mono-(2-ethylhexyl) phthalate, respectively. Compared to single PAEs, the concentration of PAEs and their metabolites in the roots treated with PS-NPs showed a great increase, while they exhibited a significant decline in the presence of PS-MPs. Principal coordinate analysis and permutational multivariate analysis of variance demonstrated that PS size were the major factor that induced oxidative damage, and altered the endogenous homeostasis of wheat roots. The increase in PS size positively promoted the relative abundance of dominant endophytes. Specifically, Proteobacteria. Proteobacteria were the most important in the symbiosis survival, which had a great impact on the microbial community and diversity. Therefore, PS and PAEs could affect the endophytes directly and indirectly. Structural equation modeling further implied that these endophytic bacteria, along with antioxidant enzymes such as superoxide dismutase which were regulated by non-enzymatic mechanisms, promoted root biomass increase. These results indicated a synergistic resistance mechanism between antioxidant enzymes and endophytic bacteria in response to environmental stress.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Analysis of endophytic bacterial flora of mulberry cultivars susceptible and resistant to bacterial wilt using metagenomic sequencing and culture-dependent approach

Endophytes have a wide range of potential in maintaining plant health and sustainable agricultural environmental conditions. In this study, we analysed the diversity of endophytic bacteria in four mulberry cultivars with different resistance capacity against bacterial wilt using metagenomic sequencing and culture-dependent approaches. We further assessed the role of 11 shared genera in the control of bacterial wilt of mulberry. The results of the present study showed that Actinobacteria, Firmicutes, and Proteobacteria were the three dominant phyla in all communities, with the representative genera Acinetobacter and Pseudomonas. The diversity analysis showed that the communities of the highly and moderately resistant varieties were more diverse compared to those of the weakly resistant and susceptible varieties. The control tests of mulberry bacterial wilt showed that Pantoea, Atlantibacter, Stenotrophomonas, and Acinetobacter were effective, with a control rate of over 80%. Microbacterium and Kosakonia were moderately effective, with a control rate between 50 and 80%. At the same time, Escherichia, Lysinibacillus, Pseudomonas, and Rhizobium were found to be less effective, with a control rate of less than 40%. In conclusion, this study provides a reasonable experimental reference data for the control of bacterial wilt of mulberry.

Identification of a 17β-estradiol-degrading Microbacterium hominis SJTG1 with high adaptability and characterization of the genes for estrogen degradation

Environmental estrogen contamination poses severe threat to wildlife and human. Biodegradation is an efficient strategy to remove the wide-spread natural estrogen, while strains suitable for hostile environments and fit for practical application are rare. In this work, Microbacterium hominis SJTG1 was isolated and identified with high degrading efficiency for 17β-estradiol (E2) and great environment fitness. It could degrade nearly 100% of 10 mg/L E2 in minimal medium in 6 days, and remove 93% of 1 mg/L E2 and 74% of 10 mg/L E2 in the simulated E2-polluted solid soil in 10 days. It maintained stable E2-degrading efficiency in various harsh conditions like non-neutral pH, high salinity, stress of heavy metals and surfactants. Genome mining and comparative genome analysis revealed that there are multiple genes potentially associated with steroid degradation in strain SJTG1. One 3β/17β-hydroxysteroid dehydrogenase HSD-G129 induced by E2 catalyzed the 3β/17β-dehydrogenation of E2 and other steroids efficiently. The transcription of hsd-G129 gene was negatively regulated by the adjacent LysR-type transcriptional regulator LysR-G128, through specific binding to the conserved site. E2 can release this binding and initiate the degradation process. This work provides an efficient and adaptive E2-degrading strain and promotes the biodegrading mechanism study and actual remediation application.

Effects of four endophytic bacteria on cadmium speciation and remediation efficiency of Sedum plumbizincicola in farmland soil

Cadmium (Cd) pollution in farmland soils severely affects agricultural production safety, thereby threatening human health. Sedum plumbizincicola is a Cd and Zn hyperaccumulator commonly used for the phytoremediation of Cd-contaminated soil. This study was aimed to improve the remediation effect of S. plumbizincicola on Cd-contaminated farmland soil and provide a theoretical basis for the enhancement of endophytic bacteria in the repair of Cd-contaminated soil with S. plumbizincicola. Four kinds of endophytic bacteria, namely Buttiauxella, Pedobacter, Aeromonas eucrenophila, and Ralstonia pickettii, were used, and soil culture experiments and pot experiments were conducted to explore the effects of endophytic bacteria on soil Cd speciation and phytoremediation efficiency of Cd-contaminated farmland soils. Under the experimental conditions, after inoculation with endophytic bacteria, the soil pH was effectively reduced, content of weak acid-extracted Cd and oxidizable Cd increased, and content of reducible Cd and residual Cd decreased. Soil Cd activity was increased, and the availability coefficient of soil Cd increased by 1.15 to 6.41 units compared with that of the control (CK₂). Compared with CK₂, the biomass of S. plumbizincicola significantly increased by 23.23-55.12%; Cd content in shoots and roots of S. plumbizincicola increased by 29.63-46.01% and 11.42-84.47%, respectively; and bioconcentration factor was 2.13 to 2.72 times that of CK₂. The Cd removal rate of S. plumbizincicola monocropping was 48.25%. When S. plumbizincicola was planted with inoculating endophytic bacteria, the Cd removal rate in the soil reached 61.18-71.49%, which was significantly higher than that of CK₂ (p < 0.05). The treatment with endophytic bacteria activated soil Cd, promoted the growth of S. plumbizincicola, increased its Cd content, and enhanced the phytoremediation of Cd-contaminated farmland soil. Therefore, endophytic bacteria can be used to improve the remediation efficiency of S. plumbizincicola in Cd-contaminated farmland soils.

Plant growth-promoting actinobacterial inoculant assisted phytoremediation increases cadmium uptake in Sorghum bicolor under drought and heat stresses

In this study, two proficient Cadmium (Cd) resistant and plant growth-promoting actinobacterial strains were isolated from metal-polluted soils and identified as Streptomyces sp. strain RA04 and Nocardiopsis sp. strain RA07. Multiple abiotic stress tolerances were found in these two actinobacterial strains, including Cd stress (CdS), drought stress (DS) and high-temperature stress (HTS). Both actinobacterial strains exhibited multifarious plant growth-promoting (PGP) traits such as phosphate solubilization, and production of indole-3-acetic acid, siderophores and 1-aminocyclopropane-1-carboxylate deaminase under CdS, DS and HTS conditions. The inoculation of strains RA04 and RA07 significantly increased Sorghum bicolor growth and photosynthetic pigments under CdS, DS, HTS, CdS + DS and CdS + HTS conditions as compared to their respective uninoculated plants. The actinobacterial inoculants reduced malondialdehyde concentration and enhanced antioxidant enzymes in plants cultivated under various abiotic stress conditions, indicating that actinobacterial inoculants reduced oxidative damage. Furthermore, strains RA04 and RA07 enhanced the accumulation of Cd in plant tissues and the translocation of Cd from root to shoot under CdS, CdS + DS and CdS + HTS treatments as compared to their respective uninoculated plants. These findings suggest that RA04 and RA07 strains could be effective bio-inoculants to accelerate phytoremediation of Cd polluted soil even in DS and HTS conditions.

Root-associated microbiota drive phytoremediation strategies to lead of Sonchus Asper (L.) Hill as revealed by intercropping-induced modifications of the rhizosphere microbiome

Intercropping or assistant endophytes promote phytoremediation capacities of hyperaccumulators and enhance their tolerance to heavy metal (HM) stress. Findings from a previous study showed that intercropping the hyperaccumulator Sonchus asper (L.) Hill grown in HM-contaminated soils with maize improved the remediating properties and indicated an excluder-to-hyperaccumulator switched mode of action towards lead. In the current study, RNA-Seq analysis was conducted on Sonchus roots grown under intercropping or monoculture systems to explore the molecular events underlying this shift in lead sequestering strategy. The findings showed that intercropping only slightly affects S. asper transcriptome but significantly affects expression of root-associated microbial genomes. Further, intercropping triggers significant reshaping of endophytic communities associated with a 'root-to-shoot' transition of lead sequestration and improved phytoremediation capacities of S. asper. These findings indicate that accumulator activities of a weed are partially attributed to the root-associated microbiota, and a complex network of plant-microbe-plant interactions shapes the phytoremediation potential of S. asper. Analysis showed that intercropping may significantly change the structure of root-associated communities resulting in novel remediation properties, thus providing a basis for improving phytoremediation practices to restore contaminated soils.

Fungal Seed Endophyte FZT214 Improves Dysphania ambrosioides Cd Tolerance Throughout Different Developmental Stages

Phytoremediation is a promising remediation method of heavy metal (HM)-contaminated soils. However, lower HM tolerance of metal accumulator inhibits its practical application and effects. The current study was aimed to illustrate the role of fungal seed endophyte (FZT214) in improving Dysphania ambrosioides Cd tolerance during different developmental stages under various Cd stresses (5, 15, 30 mg kg-1) by pot experiments. The results showed that FZT214 significantly (p < 0.05) improved the host plant's growth at the flowering and fruiting stage in most of the treatment, while at the growing stage the increase was less (p > 0.05). The seed yield was also improved (p < 0.05) in the FZT214-inoculated plants (E+) and induced early flowering was observed. Moreover, the inoculation also positively affected total chlorophyll content, antioxidant process, and lipid peroxidation in most of the treatments throughout three developmental stages. Not all but in most cases, IAA and GA were more in E+ plants while JA was more in the E- plants (non-inoculated plants) during three developmental stages. The results suggested that the colonization of FZT214 to the D. ambrosioides might trigger multiple and comprehensive protective strategies against Cd stress, which mainly include activation of the dilution effects, induced biochemical changes to overcome damage from Cd toxicity, and alteration of the endogenous phytohormones. FZT214 can find competent application in the future to improve the growth of other crop plants.

Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

Effects of Herbaspirillum sp. p5-19 assisted with alien soil improvement on the phytoremediation of copper tailings by Vetiveria zizanioides L

Microbial assisted phytoremediation and reclamation are both potential contaminated soil remediation technologies, but little is known about the combined application of the two technologies on real contaminated soils. This study investigated the potential of Herbaspirillum sp. p5-19 (p5-19) assisted with alien soil improvement on improving stress tolerance and enhancing the accumulation of Mn, Cu, Zn, and Cd by Vetiveria zizanioides L. in copper tailings. Phytoremediation potential was evaluated by plant biomass and the ability of plants to absorb and transfer heavy metals. Results showed that the biomass was increased by 19.64-173.81% in p5-19 inoculation treatments with and without alien soil improvement compared with control. Meanwhile, photosynthetic pigment contents were enhanced in co-inoculation treatment (p5-19 with alien soil improvement). In addition, the malondialdehyde (MDA) content was decreased, and the activities of antioxidant enzymes such as ascorbate peroxidase (APX), superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased in p5-19 treatment, thereby alleviating the oxidative stress. Moreover, co-inoculation significantly (p < 0.05) increased the concentrations of Mn, Cu, Zn, and Cd in the roots and shoots of V. zizanioides. In particular, the highest concentrations of Mn, Zn, and Cd in the shoots (roots) were obtained in covering 10 cm combined with p5-19 inoculation treatment, which were 4.44- (2.71-), 4.73- (3.87-), and 5.93- (4.35-) fold as that of the controls, respectively. These results provided basis for the change of phytoremediation ability of V. zizanioides after inoculation. We concluded that p5-19 assisted with alien soil improvement was a potential strategy for enhancing phytoremediation ability in tailings.

Enhanced Cd phytostabilization and rhizosphere bacterial diversity of Robinia pseudoacacia L. by endophyte Enterobacter sp. YG-14 combined with sludge biochar

Robinia pseudoacacia L., a pioneer woody legume grown in mining areas, has been recognized as a remarkable accumulator of various heavy metals. Compared with other hazardous heavy metals (HMs), it is of low capacity in accumulating Cd, which, as a result, may hinder the phytoremediation efficiency. To enhance R. pseudoacacia's uptake efficiency of Cd, the individual effects of various rhizobia and arbuscular mycorrhizal fungi have been reported, however, the combined influence of endophytes and biochar receives little attention. In the current study, a Cd-adsorbing endophyte Enterobacter sp. YG-14 was inoculated to R. pseudoacacia, and its extraordinary effect on increasing R. pseudoacacia's Cd uptake was found, which was ascribed to the reinforced root Cd chelation by the strain through secreting siderophores/LMWOAs. Further, P-enriched sludge biochar was applied along with YG-14 to form a combined biochar-endophyte-accumulator system, in which biomineralization were reinforced (i.e. CdCO₃ and Cd₂P₂O₇ were generated), as the total and acid-soluble Cd in rhizosphere were reduced by 61.75% and 69.01% respectively, and soil's bacterial diversity was further improved with diversified N₂-fixing microbial biomarkers. Multiple synergistic effects (E > 0) were also found, with the optimum performance on plant growth parameters (increased by 39.61%-561.91%) in comparison to the control group. Moreover, the system exhibited a preferable Cd phytostabilization capacity with the highest increase (81.42%) in Cd accumulation and a significant reduction (72.73%) in Cd root-to-shoot translocation.

Long-term effects of phytoextraction by a poplar clone on the concentration, fractionation, and transportation of heavy metals in mine tailings

Mine tailings are one of main causes of diffused heavy metal pollution since the heavy metals in there may acquire mobility. The current knowledge of the processes at work in long-term phytoremediation by woody species remains insufficient. Through a 4-year field study, we evaluated the phytoextraction efficiency of Populus deltoides CL. 'Xianglin 90' grown on a mine tailing co-polluted by Cd, Cu, Cr, Ni, Pb, and Zn. The concentrations of Cd, Cu, Ni, Pb, and Zn in the rhizospheric soil were reduced by amounts ranging from 12.86 to 42.19% during the study period. Bioconcentration factors and translocation factors showed that the accumulation of Cd and Zn occurring in the shoots was the most effective. Combined with the considerable biomass produced by poplar, the extracted amounts of Cd and Zn could reach 0.61 g and 10.66 g plant^-1, respectively, in which the shoots account for 77.3% (Cd) and 89.0% (Zn) of the overall extraction amounts. Acid-soluble Cd and Zn increased by 5.49% and 4.29%, respectively, in the rhizosphere compared to the bulk soil, indicating that poplar enhanced the mobility of Cd and Zn in the rhizosphere, which explained its ability for bioaccumulation and root-shoot translocation. Moreover, calculated time required to address the issue of Cd and Zn pollution was theoretically shortened by more than half from 2015 to 2019. This study brings new insights into the long-term effects of phytoextraction on the concentration, fractionation, and transportation of heavy metals and confirms the potential of poplar as a Cd and Zn remediation species.

Deciphering the Endophytic and Rhizospheric Microbial Communities of a Metallophyte Commelina communis in Different Cu-Polluted Soils

Metallophytes microbiota play a key role in plant growth and resistance to heavy metal stress. Comparing to the well-studied single or some specific plant growth-promoting (PGP) bacterial strains, our current understanding of the structural and functional variations of microbiome of metallophytes is still limited. Here, we systematically investigated the endophytic and rhizosphere bacterial community profiles of a metallophyte Commelina communis growing in different Cu-polluted soils by high-throughput sequencing technology. The results showed that the rhizosphere communities of C. communis exhibited a much higher level of diversity and richness than the endosphere communities. Meanwhile, shifts in the bacterial community composition were observed between the rhizosphere and endosphere of C. communis, indicating plant compartment was a strong driver for the divergence between rhizosphere and endosphere community. Among the environmental factors, soil Cu content, followed by OM, TP and TN, played major roles in shaping the bacterial community structure of C. communis. At the highly Cu-contaminated site, Pseudomonas and Sphingomonas were the predominant genera in the endophytic and rhizospheric bacterial communities, respectively, which might enhance copper tolerance as PGP bacteria. In summary, our findings will be useful to better understand metallophyte–microbe interactions and select suitable bacterial taxa when facilitating phytoremediation.

Influence of Rahnella aquatilis on arsenic accumulation by Vallisneria natans (Lour.) Hara for the phytoremediation of arsenic-contaminated water

Vallisneria natans (Lour.) Hara is a suitable submerged plant for the phytoremediation of As-contaminated water. Rahnella aquatilis is one of the plant growth-promoting rhizobacteria. Influences of R. aquatilis on the arsenic accumulation and detoxification of V. natans were investigated. The results showed that As accumulation by V. natans could be significantly improved after R. aquatilis inoculated at the lower level of As (< 2 mg/L). At 0.5, 1, and 2 mg/L As levels, the As concentrations of V. natans with R. aquatilis were respectively 100.40%, 57.96%, and 22.62% higher than that of V. natans with no R. aquatilis. The concentration of As in V. natans was increased with the increasing the As concentration up to 1 mg/L, but it was decreased at 2 mg/L As. The correlation analysis showed that the As accumulated in the plant was positive correlated (R² = 0.977, p < 0.01) with indole-3-acetic acid (IAA) produced by R. aquatilis under different As levels. IAA may be the major factor affecting the As accumulation of V. natans. The results of malondialdehyde and superoxide dismutase, hydrogen peroxidase, and ascorbate peroxidase indicated that IAA produced by R. aquatilis had alleviated the arsenic stress on V. natans. The synthesis of IAA by R. aquatilis was related to the As levels. When the As was at 2 mg/L, the IAA that produced by R. aquatilis decreased and the promotion of R. aquatilis on As accumulation by V. natans reduced. However, R. aquatilis has a positive influence on the arsenic accumulation by V. natans at the lower As levels (< 2 mg/L), and it may be a potentially useful way to improve the removal of arsenic from contaminated water using submerged plants.

Impacts and tolerance responses of Coprinus comatus and Pleurotus cornucopiae on cadmium contaminated soil

Large amounts of cadmium (Cd) have been discharged into soil with the rapid development of industry. In this study, we revealed the impacts of Coprinus comatus (C. comatus) and Pleurotus cornucopiae (P. cornucopiae) on soil and the tolerance responses of macrofungi in the presence of Cd by the analysis of soil biochemical properties and macrofungi growth indexes. Results showed that with the cultivation of C. comatus and P. cornucopiae, the HOAc-extractable Cd in soil individually reduced by 9.53% and 11.35%, the activities of soil urease, acid phosphatase, dehydrogenase, and Fluorescein diacetate (FDA) hydrolysis increased by 18.11-101.45%, 8.39-18.24%, 9.37-55.50% and 28.94-41.92%, respectively. Meanwhile, different soil bacterial communities were observed with various macrofungi cultivations. Also, Cd accumulation significantly enhanced the macrofungi antioxidant enzyme activities, which increased by 24.10-45.43%, 30.11-61.53% and 7.03-26.81% for catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities in the macrofungi, respectively. Moreover, the enhanced macrofungi endophytic bacterial diversities with Cd existence was firstly observed in the present experiment. These findings revealed the possible Cd resistance mechanisms in macrofungi, suggesting C. comatus and P. cornucopiae were promising ameliorators for Cd contaminated soil.

Insights into the effects of heavy metal pressure driven by long-term treated wastewater irrigation on bacterial communities and nitrogen-transforming genes along vertical soil profiles

Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss.

Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach

To ensure food security for the ever-increasing world's population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth-promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.

Combined application of Bacillus sp. MN-54 and phosphorus improved growth and reduced lead uptake by maize in the lead-contaminated soil

Lead (Pb) is considered an important environmental contaminant due to its considerable toxicity to living organisms. It can enter and accumulate in plant tissues and become part of the food chain. In the present study, individual and combined effects of Bacillus sp. MN-54 and phosphorus (P) on maize growth and physiology were evaluated in Pb-contaminated soil. A pristine soil was artificially contaminated with two levels of Pb (i.e., 250 and 500 mg kg^-1 dry soil) and was transferred to plastic pots. Bacillus sp. MN-54 treated and untreated maize (DK-6714) seeds were planted in pots. Recommended doses of nutrients (N and K) were applied in each pot while P was applied in selective pots. Results showed that Pb stress hampered the maize growth and physiological attributes in a concentration-dependent manner, and significant reductions in seedling emergence, shoot and root lengths, fresh and dry biomasses, leaf area, chlorophyll content, rate of photosynthesis, and stomatal conductance were recorded compared with control. Application of Bacillus sp. MN-54 or P particularly in combination significantly reduced the toxic effects of Pb on maize. At higher Pb level (500 mg kg^-1), the combined application effectively reduced Pb uptake up to 42.4% and 50% by shoots, 30.8% and 33.9% by roots, and 18.4% and 26.2% in available Pb content in soil after 45 days and 90 days, respectively compared with that of control. Moreover, the use of Bacillus sp. MN-54 significantly improved the P uptake by maize plants by 44.4% as compared with that of control. Our findings suggest that the combined use of Bacillus sp. MN-54 and P could be effective and helpful in improving plant growth and Pb immobilization in Pb-contaminated soil.

Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere

Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.

Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.

Genomic diversity of bacteriophages infecting Microbacterium spp

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association

This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.

Naturally selected dominant weeds as heavy metal accumulators and excluders assisted by rhizosphere bacteria in a mining area

Managers need more practical and promising plants for use in heavy metal phytoremediation. Although previous studies have identified the potential of some weeds and microbial strains in phytoremediation, the potential of dominant weeds and the relationship between weeds and their rhizosphere bacterial strains are still unknown. In our study, we examined dominant weeds in the Dabaoshan mine located in Guangdong province, China to test their abilities as heavy metal accumulators and excluders. Results suggest that Ludwigia prostrata exhibited the highest potential for accumulating Cu, Pb and Zn compared with the other plants. Specifically, L. prostrata accumulated 71.58, 130.76 and 454.72 mg kg^-1 of Cu, Pb and Zn, respectively; the species' translocation factor of Zn was 2.04, indicating a high accumulation of Zn. In contrast, the Cd translocation factor (TF) of Digitaria sanguinalis was 0.18, significantly lower than that of other plant species examined. Our results suggest that Ludwigia prostrata hyperaccumulates Zn and may also serve as a potential candidate remediation plant for Cu and Pb due to its high absolute accumulation amount of Cu and Pb, while Digitaria sanguinalis may be a potential candidate as a Cd excluder. We also found that rhizosphere bacterial communities were shaped by individual dominant plant species. Chloroflexi was the most dominant phylum in accumulator plant such as Fimbristylis miliacea, while Cyanobacteria was the most dominant phylum in excluder plant such as Digitaria sanguinalis. Our study provides insights for selecting new weedy forbs and grasses, rhizosphere bacterial species and developing approaches for phytoremediation and phytostabilization.

Effects of endophytes inoculation on rhizosphere and endosphere microecology of Indian mustard (Brassica juncea) grown in vanadium-contaminated soil and its enhancement on phytoremediation

We investigated the effects of endophytes inoculation on ecological factors such as root morphology, rhizosphere soil properties, heavy metal speciation, and rhizosphere and endophytic bacterial communities and their role on phytoremediation. Indian mustards were grown for two months in V-contaminated soil with three treatments (control, inoculation with Serratia PRE01 or Arthrobacter PRE05). Inoculation with PRE01 and PRE05 increased organic matter content by 6.94% and 4.6% respectively and significantly increased bioavailability of heavy metals in rhizosphere soils. Despite the endophyte inocula failed to flourish as stable endophytes, they significantly affected the specific composition and diversity of endophytic bacterial communities in roots, with no significant effect on rhizosphere bacterial communities. The test strains could greatly increase plant growth promotion-related biomarkers in the endosphere, especially those associated with Pseudomonas and Microbacterium genera. PICRUSt analysis predicted high relative abundances of functional genes related to environmental information processing especially in the endophytic microbiota. More biomass production (12.0%-17.4%) and total metals uptake (24.2%-32.0%) were acquired in inoculated treatments. We conclude that endophyte PRE01 or PRE05 inoculation could effectively enhance phytoremediation of V-contaminated soil by improving the rhizosphere and endosphere microecology without causing any ecological damage.

Indigenous strain Bacillus XZM assisted phytoremediation and detoxification of arsenic in Vallisneria denseserrulata

The symbiosis between Vallisneria denseserrulata and indigenous Bacillus sp. XZM was investigated for arsenic removal for the first time. It was found that the native bacterium was able to reduce arsenic toxicity to the plant by producing higher amount of extra cellular polymeric substances (EPS), indole-3-acetic acid (IAA) and siderosphore. Interestingly, V. denseserrulata-Bacillus sp. XZM partnership showed significantly higher arsenic uptake and removal efficiency. The shift in FT-IR spectra indicated the involvement of amide, carboxyl, hydroxyl and thiol groups in detoxification of arsenic, and the existence of an arsenic metabolizing process in V. denseserrulata leaves. The scanning electron microscopy (SEM) images further confirmed that the bacterium colonized on plant roots and facilitated arsenic uptake by plant under inoculation condition. In plant, most of the arsenic existed as As(III) (85%) and was massively (>77%) found in vacuole of particularly leaves cells. Thus, these findings are highly suggested for arsenic remediation in the constructed wetlands.

Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.

Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery

We report the complete annotated genome sequence of Microbacterium foliorum NRRL B-24224, a type strain isolated from the phyllosphere of grasses and a commonly used host for bacteriophage discovery. The genome contains no identifiable prophage or CRISPR or restriction-modification system, which suggests that it may continue to be a fruitful host for phage discovery.

We report the complete annotated genome sequence of Microbacterium foliorum NRRL B-24224, a type strain isolated from the phyllosphere of grasses and a commonly used host for bacteriophage discovery. The genome contains no identifiable prophage or CRISPR or restriction-modification system, which suggests that it may continue to be a fruitful host for phage discovery.

Endophytic fungal community of Dysphania ambrosioides from two heavy metal-contaminated sites: evaluated by culture-dependent and culture-independent approaches

Endophytic fungal communities of Dysphania ambrosioides, a hyperaccumulator growing at two Pb-Zn-contaminated sites, were investigated through culture-dependent and culture-independent approaches. A total of 237 culturable endophytic fungi (EF) were isolated from 368 tissue (shoot and roots) segments, and the colonization rate (CR) ranged from 9.64% to 65.98%. The isolates were identified to 43 taxa based on morphological characteristics and rDNA ITS sequence analysis. Among them, 13 taxa (30.23%) were common in plant tissues from both sites; however, dominant EF were dissimilar. In culture-dependent study, 1989 OTUs were obtained through Illumina Miseq sequencing, and dominant EF were almost same in plant tissues from both sites. However, some culturable EF were not observed in total endophytic communities. We suggest that combination of both culture-dependent and culture-independent methods will provide more chances for the precise estimation of endophytic fungal community than using either of them. The tissue had more influence on the culturable fungal community structure, whereas the location had more influence on the total fungal community structure (including culturable and unculturable). Both culture-dependent and culture-independent studies illustrated that endophytic fungal communities of D. ambrosioides varied across the sites, which suggested that HM concentration of the soil may have some influence on endophytic fungal diversity.