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Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.

International Journal of Biological Macromolecul

Additional file 1. Transmission electron microscope image of the silver nanoparticles used in the study. Nanoparticles were obtained in solid form from US Research Nanomaterials, Inc. (Houston, TX, USA), and were applied to soil in this form.

Air pollution, containing fossil fuel-related volatile organic compounds (VOCs), constitutes a major problem in most urban areas. Worldwide, more people die from exposure to air pollution than from malaria and HIV infection together. Many years of research show that plant–microbe interactions can be exploited to significantly enhance phytoremediation of contaminated environments. Microorganisms living on plant leaves constitute promising candidates to detoxify harmful VOCs and promote plant growth. Hedera helix, an evergreen plant known for its hardiness and climbing ability, proves to be an excellent host species in the context of phytoremediation of air pollution. We employed 16S rRNA gene amplicon-based metagenomics to characterize the taxonomic structure of phyllospheric microbial communities associated with H. helix. Further, we investigated 33 bacterial isolates from 8 different genera using culture-dependent approaches and whole genome sequencing. Our results indicate that the relative composition of the H. helix phyllobiome is similar to that of the model plant Arabidopsis thaliana. The presence of pathways related to detoxification of fossil fuel-related VOCs could be confirmed by genome-level analyses of bacterial isolates showing a high in vitro capacity to metabolize selected VOCs and promote plant growth. We provide an integrated description of the H. helix phyllobiome, including the identification of interesting bacteria with significant potential as inoculants in phytoremediation approaches. Het Fonds voor Wetenschappelijk Onderzoek – Vlaanderen (FWO)

Air pollution, containing fossil fuel-related volatile organic compounds (VOCs), constitutes a major problem in most urban areas. According to recent data, more people die from exposure to air pollution than from malaria and HIV infection together. Many years of research show that plant–microbe interactions can be exploited to significantly enhance phytoremediation of contaminated environments. Microorganisms living on plant leaves constitute promising candidates to detoxify harmful VOCs and promote plant growth. Hedera helix, an evergreen plant known for its hardiness and climbing ability, proves to be an excellent host species in the context of phytoremediation of air pollution. We employed 16S rRNA gene amplicon-based metagenomics and real-time PCR to characterize the taxonomic structure of phyllospheric microbial communities associated with H. helix, and compared the communities present at polluted high-traffic locations with non-polluted sites. Further, we investigated bacterial isolates using culture-dependent approaches and sequenced the genomes of promising bacteria with regard to phytoremediation applications. Our results indicate that Actinobacteria, Firmicutes and Betaproteobacteria are more abundantly present on H. helix leaves in a polluted environment. Moreover, the relative composition of the H. helix phyllobiome appears to be similar to that of the model plant Arabidopsis thaliana. We further show that air pollution increases the prevalence of bacterial functional traits affiliated to plant growth and detoxification of fossil fuel-related VOCs. The presence of relevant pathways could be confirmed by genome-level analyses of bacterial isolates showing a high in vitro capacity to metabolize selected VOCs and promote plant growth. In conclusion, an integrated description of the H. helix phyllobiome is presented, including the identification of interesting bacteria with significant potential as inoculants in phytoremediation approaches. This work is supported by the Hasselt University Methusalem project 08M03VGRJ

Additional file 1. Soil characteristics analyzed in 2012 and 2013. a organic matter, b electrical conductivity of a saturated soil paste extract (ECe), c Total soil N by Kjeldahl method.

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies. This work was supported by a PhD grant to ST and a post doc grant for NW from the Fund for Scientific Research Flanders, Belgium (FWO-Vlaanderen) and the Methusalem project 08M03VGRJ.

Additional file 2. VAP test - Comparison of the root system architectures. Vertical Agar Plate test. Comparison of the root system architectures of non-inoculated and inoculated Arabidopsis seedlings through the 2D pictures created with the RootNav image analysis tool (University of Nottingham).

Since air pollution has been linked to a plethora of human health problems, strategies to improve air quality are indispensable. Despite the complexity in composition of air pollution, phytoremediation was shown to be effective in cleaning air. Plants are known to scavenge significant amounts of air pollutants on their aboveground plant parts. Leaf fall and runoff lead to transfer of (part of) the adsorbed pollutants to the soil and rhizosphere below. After uptake in the roots and leaves, plants can metabolize, sequestrate and/or excrete air pollutants. In addition, plant-associated microorganisms play an important role by degrading, detoxifying or sequestrating the pollutants and by promoting plant growth. In this review, an overview of the available knowledge about the role and potential of plant-microbe interactions to improve indoor and outdoor air quality is provided. Most importantly, common air pollutants (particulate matter, volatile organic compounds and inorganic air pollutants) and their toxicity are described. For each of these pollutant types, a concise overview of the specific contributions of the plant and its microbiome is presented. To conclude, the state of the art and its related future challenges are presented. This work has been financially supported by the UHasselt Methusalem project 08M03VGRJ

Door militaire activiteit en industriële productie zijn wereldwijd bodems en grondwater vervuild met explosieven, waaronder 2,4-Dinitrotolueen. Fytoremediatie van explosieven wordt gelimiteerd door hun extreme bioresistentie en toxiciteit. Daarom kan een bacterie-gestimuleerde fytoremediatie een mogelijke oplossing bieden, waarbij bacteriën met de gewenste afbraakcapaciteiten zorgen voor een versnelde fytodegradatie. Deze studie onderzoekt de geno- en fenotypische karakterisatie van bodembacteriën, met potentieel om 2,4-DNT af te breken. Selectieve aanrijkingen en auxanografie toonden aan dat 2,4-DNT tolerante bacteriën aanwezig zijn in de bodemmonsters, verzameld op een met explosieven vervuild terrein. Met HPLC werd bevestigd dat Pseudomonas tolaassi en Burkholderia fungorum de capaciteit bezitten om 2,4-DNT te transformeren via een oxidatieve denitratie van de ring. Tot slot werden plantengroei-promoverende bacteriën geïdentificeerd die de wortellengte van A. thaliana zaailingen, bl

We explored the seed-associated bacterial endophytic microbiome in seeds of the endemic holoparasitic species Cistanche armena from a saline and arid habitat in Armenia. A combination of culture-dependent and molecular techniques was employed for identifying the seed endomicrobiome (culturable and unculturable). From surface-sterilized seeds, 10 phyla, comprising 256 endophytic bacterial genera, were identified. Of the culturable strains, we also investigated the plant growth-promoting (PGP) traits. Most of the isolates were spore forming, halotolerant and alkaliphile Bacillus spp., indicating that the endophytic bacteria of C. armena seeds own traits related to the natural habitat of their host plant. Our results confirm that Bacillus species are common and dominated endophytes from plants growing on saline and arid soils. Pantoea spp. and Stenotrophomonas spp. are more favourable PGP endophytes in seeds of C. armena. The PGP traits of these bacteria, such as production of indole, a precursor of auxin, ACC-deaminase and organic acids have the potential to improve the tolerance of their host plants against the abiotic stresses present in their natural habitat. To the best of our knowledge, this is the first report concerning bacterial seed endophytes of the C. armena. The manuscript was prepared under ‘Partnership agreement governing the joint supervision and awarding of a doctorate diploma between Jan Kochanowski University in Kielce (Poland) and Hasselt University (Belgium)’ (K.P.). We thank Dr. Yuliya Krasylenko for taking photographs under a zoom microscope. The author acknowledges financial support through the project ‘Development Accelerator of the Jan Kochanowski University of Kielce’, co-financed by the European Union under the European Social Fund (K.P., POWR.03.05.00-00-Z212/18, 2019– 2023). This study was supported by grants from the Jan Kochanowski University (K.R., 666 065, 2019) and (W.K., K.P., SUPB.RN. 21.235, 2021-2022). The field research in this study in Armenia was partially financed by the National Geographic grant (R.P., GEFNE 192-16, 2017). This study was also supported by a BOF-BILA grant from Hasselt University Belgium BOF21BL12 (K.P., J.V., 2021–2022) and the Hasselt University Methusalem project (J.V., 08M03VGRJ).

The mammalian holobiont harbors a complex and interdependent mutualistic gut bacterial community. Shifts in the composition of this bacterial consortium are known to be a key element in host health, immunity and disease. Among many others, dietary habits are impactful drivers for a potential disruption of the bacteria-host mutualistic interaction. In this context, we previously demonstrated that a high-salt diet (HSD) leads to a dysbiotic condition of murine gut microbiota, characterized by a decrease or depletion of well-known health-promoting gut bacteria. However, due to a controlled and sanitized environment, conventional laboratory mice (CLM) possess a less diverse gut microbiota compared to wild mice, leading to poor translational outcome for gut microbiome studies, since a reduced gut microbiota diversity could fail to depict the complex interdependent networks of the microbiome. Here, we evaluated the HSD effect on gut microbiota in CLM in comparison to wildling mice, which harbor a natural gut ecosystem more closely mimicking the situation in humans. Mice were treated with either control food or HSD and gut microbiota were profiled using amplicon-based methods targeting the 16S ribosomal gene. In line with previous findings, our results revealed that HSD induced significant loss of alpha diversity and extensive modulation of gut microbiota composition in CLM, characterized by the decrease in potentially beneficial bacteria from Firmicutes phylum such as the genera Lactobacillus, Roseburia, Tuzzerella, Anaerovorax and increase in Akkermansia and Parasutterella. However, HSD-treated wildling mice did not show the same changes in terms of alpha diversity and loss of Firmicutes bacteria as CLM, and more generally, wildlings exhibited only minor shifts in the gut microbiota composition upon HSD. In line with this, 16S-based functional analysis suggested only major shifts of gut microbiota ecological functions in CLM compared to wildling mice upon HSD. Our findings indicate that richer and wild-derived gut microbiota is more resistant to dietary interventions such as HSD, compared to gut microbiota of CLM, which may have important implications for future translational microbiome research. A.C. was supported by the Research Foundation Flanders (FWO), Belgium (Project ID 11L8322N). J.V. was supported by UHasselt Methusalem project 08M03VGRJ and by a BOF grant (ADMIRE, Project ID 21GP17BOF) from Hasselt University. D.N.M. was supported by the Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK, Project ID 81Z0100106) and by the Deutsche Forschungsgemeinschaft (DFG) (DFG SFB 1470, A06). S.P.R. was supported by the DFG Emmy Noether-Programm RO 6247/1-1 (Project ID 446316360) and DFG (DFG SFB1160 IMPATH, Project ID 256073931) and TRR 359 PILOT project (Project ID 491676693). M.K. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project ID 640116), by a SALK-grant from the government of Flanders, by an Odysseus-grant (Project ID G0G1216FWO) and senior research project (Project ID G080121N) of the FWO and by a BOF grant (ADMIRE, Project ID 21GP17BOF) from Hasselt University

Endophytes within plants are known to be crucial for plant fitness, and while their presence and functions in many compartments have been studied in depth, the research on seed endophytes is still limited. This work aimed to characterize the seed endophytic and rhizospheric bacterial community of two Noccaea caerulescens Pb-Zn hyperaccumulator populations, growing on two heavy-metal-polluted sites in Belgium. Cultured representatives were evaluated for their potential to enhance seed germination and root length of the model species Arabidopsis thaliana. The results indicated that the community structure within the seed is conserved between the two locations, comprising mainly of Proteobacteria (seeds), and Actinobacteria in the bulk soil. Root length of A. thaliana was significantly increased when inoculated with Sphingomonas vulcanisoli. The results of this paper offer insights into the importance of the selection of the core seed endophytic microbiome and highlight the precarious symbiotic relationship they have with the plant and seed. The research was funded by BOF Special Research Fund to T.L. from Hasselt University and UHasselt Methusalem project 08M03VGRJ to J.V.

BACKGROUND: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce. OBJECTIVES: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families. METHODS: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI). RESULTS: Two diversity indices were negatively associated with placental black carbon [Shannon: -4.38% (95% CI: -8.31%, -0.28%); Simpson: -0.90% (95% CI: -1.76%, -0.04%)], cord blood black carbon [Shannon: -3.38% (95% CI: -5.66%, -0.84%); Simpson: -0.91 (95% CI: -1.66%, -0.16%)], and urinary black carbon [Shannon: -3.39% (95% CI: -5.77%, -0.94%); Simpson: -0.89% (95% CI: -1.37%, -0.40%)]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae, and urinary black carbon with Christensenellaceae and Coriobacteriaceae; associations with cord blood black carbon were not statistically significant after correction. CONCLUSION: Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. https://doi.org/10.1289/EHP11257. ispartof: Environ Health Perspect vol:131 issue:1 pages:17010- ispartof: location:United States status: published

The inclusion of bioaugmented low-cost biochar in current wastewater treatment technologies is a promising way to enhance the removal and degradation of emerging contaminants. In this paper, the properties of two wood waste biochars (wood waste mix - AB, and date palm fiber wood - PDF), and coffee bean husks (COF), produced at four temperatures (350, 450, 500, 550°C) were compared, and investigated in the presence of Geobacter sulfurreducens or a mixed freshwater stream bacterial culture to understand their potential for the adsorption and biotransformation of two types of pesticides (thiacloprid, pirimicarb), and two pharmaceuticals (ibuprofen, diclofenac). Biochar yield was similar for all three biochars and ranged between 30 and 35%. The ash content of PDF and COF was significantly higher than AB. pH and electrical conductivity (EC) were initially high for COF (pH: 7.4–8; EC: 3–4.27 mS/cm) and PDF (pH: 7.7–10.1; EC: 4–6.24 mS/cm) after 24 h, but stabilized at neutral pH and − (550°C), and 846 mg/L sulphate (350°C). Lower pyrolysis temperatures reduced leachable anions. The biochars were highly (ultra)microporous with little meso- and macroporosity. The adsorption experiments showed that AB and COF biochars were both suited to sorb more than 90% of the initially spiked 10 ppm pirimicarb, AB removed 50.2% of the initial diclofenac concentration compared to only 5% for the no-biochar control, and both biochars could remove about 55% of the initially spiked thiacloprid, and 40% of the ibuprofen. In the presence of a mixed culture, on average 30% more thiacloprid and ibuprofen was removed from the supernatant by AB and COF than the sterile control. This work shows that selected wood-waste feedstocks and low pyrolysis temperature can produce environmentally-safe biochars that have suitable characteristics to sorb emergent pollutants from water. These materials could be further studied in multi-pollution sorption/competition experiments, and in larger environmental wastewater treatment systems.

The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally related to xenobiotics, can stimulate the presence of microbial community members, exhibiting specialized functions toward detoxifying, and thus mitigating soil toxicity. In this study, we evaluated the effects of enrichment of 4-chloro-2-methylphenoxyacetic acid (MCPA) contaminated soil (unplanted and zucchini-planted) with syringic acid (SA) on the bacterial community structure in soil, the rhizosphere, and zucchini endosphere. Additionally, we measured the concentration of MCPA in soil and fresh biomass of zucchini. The diversity of bacterial communities differed significantly between the studied compartments (i.e., unplanted soil, rhizospheric soil, and plant endosphere: roots or leaves) and between used treatments (MCPA or/and SA application). The highest diversity indices were observed for unplanted soil and rhizosphere. Although the lowest diversity was observed among leaf endophytes, this community was significantly affected by MCPA or SA: the compounds applied separately favored the growth of Actinobacteria (especially Pseudarthrobacter), while their simultaneous addition promoted the growth of Firmicutes (especially Psychrobacillus). The application of MCPA + SA together lead also to enhanced growth of Pseudomonas, Burkholderia, Sphingomonas, and Pandoraea in the rhizosphere, while SA increased the occurrence of Pseudomonas in leaves. In addition, SA appeared to have a positive influence on the degradative potential of the bacterial communities against MCPA: its addition, followed by zucchini planting, significantly increased the removal of the herbicide (50%) from the soil without affecting, neither positively nor negatively, the plant growth. The Council of the National Science Centre in Poland ETIUDA 7–funded the project “Cucurbits and their plant secondary metabolites as stimulators of biological soil remediation contaminated with phenoxy herbicides” [No. 2019/32/T/NZ9/00403]. This work was also supported by the UHasselt Methusalem project 08M03VGRJ.

The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring. The authors thanks Giovambattista Capasso from Biogem Institute for Molecular Biology and Genetics, Ariano Irpino (Italy) who allowed us to perform microscopy observations.

Pollution with microplastics (MPs), nanoplastics (NPs) and trace elements (TEs) remains a considerable threat for mangrove biomes due to their capability to capture pollutants suspended in the water. This study investigated the abundance and composition of plastics and TEs contained in the soil and pneumatophores of Avicennia alba sampled in experimental areas (hotel, market, river mouth, port, and rural areas) differentiated in anthropopressure, located in Bima Bay, Indonesia. Polymers were extracted and analyzed with the use of a modified sediment isolation method and Fourier transform infrared spectroscopy. Trace elements were detected by inductively coupled plasma optical emission spectrometry. The lowest and highest quantities of MPs in soil were recorded in rural and hotel areas, respectively. The rural site was characterized by distinct MP composition. The amounts of sediment-trapped MPs in the tested localities should be considered as high, and the recognized polymers partly corresponded with local human activity. Concentrations of seven plastic types found in plant tissues did not entirely reflect sediment pollution with nine types, suggesting a selective accumulation (particularly of polyamides and vinylidene chloride) and substance migration from other areas. Very low concentrations of non-biogenic TEs were observed, both in sediments and pneumatophores. The results highlight the relevance of environmental contamination with plastics. The research was financially supported by the Institute of Horticultural Sciences, Warsaw University of Life Sciences—SGGW (WULS—SGGW)

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. The work (proposal DOI[s]: https://doi.org/10.46936/10.25585/60001024; https://doi.org/10.46936/10.25585/60000886; https://doi.org/10.46936/10. 25585/60001401; https://doi.org/10.46936/10.25585/60001087; https:// doi.org/10.46936/10.25585/60001079; https://doi.org/10.46936/10.25585/ 60001044) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. Design and synthesis of peptide constructs were supported by the Biosystems Design program (DOE Office of Science contract DE-SC0018260) and the US Department of Energy Joint Genome Institute (DOE Office of Science contract DEAC02-05CH1123), respectively. Characterization of the peptide was supported by the Secured Biosystem Design project entitled ‘‘Rapid Design and Engineering of Smart and Secure Microbiological Systems’’ (DOE Office of Science contract DE-AC02-05CH1123). We thank the following researchers for their support of this study by providing free use of their public genome data: Kristen De-Angelis, Grace Pold, Mallory Choudoir, Camila Carlos-Shanley, Paul Carini, H. Corby C. Kistler, James Elkins, Javier A. Izquierdo, Dimitris Hatzinikolaou, Daniel Schachtman, Paul R. Jensen, Aindrila Mukhopadhyay, John Vogel, Carolin Frank, Paul M. D’Agostino, Ann M. Hirsch, Satoshi Yuzawa, Regina Lamendella, Bernhard Fuchs, Dale Pelletier, Laila P. Partida-Martinez, Cameron Currie, Seth De-Bolt, Jeff Dangl, David Mead, Susannah Tringe, David A. Baltrus, Seung Bum Kim, Linda Kinkel, Kelly Wrighton, William Mohn, Ludmila Christoserdova, Sarah Lebeis, Janet Janssen, Sandra Baena Garzon, and Nicholas Coleman. Special thanks to Marie Louise Ballon at the JGI Communications and Outreach office for all her help with the graphical abstract and many other details.

This field study aimed to assess the baseline conditions of a long-term shooting range in Argentina polluted with 428 mg kg(-1) lead (Pb) to evaluate the establishment and development of Helianthus petiolaris plants and address the efficacy of the phytomanagement strategy through: (i) element accumulation in plant tissues; (ii) rhizosphere bacterial diversity changes by Illumina Miseq (TM), and (iii) floral water and essential oil yield, composition, and element concentration by GC-MS and ICP. After one life cycle growing in the polluted sites, in the roots of Helianthus petiolaris plants, Pb concentration was between 195 and 304 mg kg(-1) Pb. Only a limited fraction of the Pb was translocated to the aerial parts. The predominance of the genus Serratia in the rhizosphere of Helianthus petiolaris plants cultivated in the polluted sites and the decrease in the essential oil yield were some effects significantly associated with soil Pb concentration. No detectable Pb concentration was found in the floral water and essential oil obtained. Extractable Pb concentration in the soil reduced between 28% and 45% after the harvest. This work was supported by the Ibero-American Development Bank under grant FONTAGRO (ATN/RF-16110-RG), Pluriannuals Projects of Investigation-CONICET (PIP0730), and the Centre for Environmental Sciences of Hasselt University, Belgium, under grant BOF-BILA No. 8546. Thanks to Andrea R. Costantino and Natalia Lazzarini from the Instituto Química del Sur, Bahía Blanca, Bs As, Argentina, for their collaboration on the GC–MS analysis of the essential oils.

Phytoextraction could be a potential management option for diffusely Cd-Zn-Pb-polluted agricultural land in Northeast Belgium. The use of high yielding crops with a sufficiently high metal accumulation is preferred as these are expected to both gradually decontaminate the soil while generating an income through biomass valorization. To find out which high biomass crop possessed the highest and most constant (in time) phytoextraction potential on these soils, different plant species and different mutants or clones of each species, were evaluated during consecutive years. Biomass production and metal accumulation of pre-selected tobacco somaclonal variants (Nicotiana tabacum L.) and pre-selected sunflower mutants (Helianthus annuus L.) were investigated for two productivity years, while the phytoextraction potential of experimental poplar (Populus) and willow (Salix) in short rotation coppice (SRC) was assessed at the end of the second cutting cycle (after two times four growing seasons). The tobacco clones and the sunflower mutants showed efficient extraction of, respectively, Cd and Zn, while the highest simultaneous extractions of Cd and Zn were gained with some SRC clones. Variation in biomass production and metal accumulation were high for all crops over the years. The highest biomass production was observed for the experimental poplar clone of the crossing type Populus deltoides (P. maximowiczii x P. trichocarpa) with 9.9 ton DW per ha per year. The remediation period to reach legal threshold values for the pseudo-total content of Cd in this specific soil was estimated to be at least 60 years. Combining estimated phytoextraction potential and economic and environmental aspects, the SRC option is proposed as the most suitable crop for implementing metal phytoextraction in the investigated area. This research was funded by the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) for JJ and by the Fund for Scientific Research Flanders (FWO Vlaanderen) for NWi. This work was financially supported by the UHasselt Methusalem project 08M03VGRJ and the European Commission under the Seventh Framework Program for Research (FP7-KBBE-266124, GREENLAND).

Pharmaceuticals in wastewater are a growing concern in wastewater treatment. Current technologies are inadequate and there is need for a new efficient treatment technology. An approach could be integrating electroconductive materials (e.g. biochar) to microbial electrochemical technologies. Electroactive bacteria (e.g. Geobacter sulfurreducens) could remediate wastewater by respiring through electrodes/electron shuttles. In this paper it is hypothesized that ibuprofen and diclofenac are removed from wastewater by anaerobic digestion (AD) in biochar included microbial electrochemical remediation (BiMER). AD of pharmaceuticals was investigated by exposing electroactive bacteria (Geobacter sulfurreducens or a mixed culture) to diclofenac or ibuprofen. After incubation, contaminant concentration was determined with HPLC and bacterial growth with Bradford assay. In adjoining experiments, similar set-ups were used with additional electroconductive material (biochar). Additionally, the AD of acetate was investigated in BiMERs with different biochar/sand mixing ratios. Neither the pure culture, nor the mixed culture could degrade the pharmaceuticals efficient in the absence of any electro-conductive material. Biochar could improve degradation, but it was dependent on the pharmaceutical. High biochar/sand mixing ratios resulted in a lower electrochemical resistance and allowed good colonisation and growth. The analysis of further experiments together with more research is needed to acquire a better understanding of the AD process.

Bioelectrochemical systems are an emerging technology for the remediation of pollutants from wastewater. Here, the degradation of pesticides in such a system is examined. HPLC, cyclic voltammetry and chronoamperometry were used as techniques. No evidence was found for the degradation of pesticides by the bacteria. Granular activated carbons are a suited substrate for bacteria in a bioelectrochemical system.

Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies. This work was financed by the Methusalem project 08M03VGRJ and was also supported by grants to STh and NW from the Fund of Scientific Research Handers. Thanks to Prof. Dr. Geert-Jan Bex for help with setting up the Flemish Supercomputer Centre (VSC) supported by the Research Foundation Handers (FWO) in partnership with the five Flemish university associations.