Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application.

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Fertilisation of agricultural soils with municipal biosolids: Glyphosate and aminomethylphosphonic acid inputs to Québec field crop soils.

Municipal biosolids (MBS) are suggested to be abundant, sustainable, inexpensive fertilisers, rich in phosphorus and nitrogen. However, MBS can also contain glyphosate and phosphonates that can degrade to AMPA. Glyphosate-based herbicides (GBH) are used in field crops all over the world. Most glyphosate generally degrades within a few weeks, mainly as aminomethylphosphonic acid (AMPA). AMPA is more persistent than glyphosate, and can accumulate from one crop year to the next. AMPA is phytotoxic even to glyphosate-resistant crops. The aims of this study were to assess whether MBS applications constitute: 1) an additional source of glyphosate and AMPA to agricultural soils with respect to GBH, 2) a significant source of trace metals, and 3) a partial replacement of mineral fertilisation while maintaining similar yields. To this end, four experimental agricultural sites were selected in Québec (Canada). Soil samples (0-20 cm) were collected to estimate the as yet unmeasured contribution of MBS application to glyphosate and AMPA inputs in agricultural soils. MBS applied in 2021 and 2022 had mean concentrations of 0.69 ± 0.53 µg glyphosate/dry g and 6.26 ± 1.93 µg AMPA/dry g. Despite the presence of glyphosate and AMPA in MBS, monitoring of these two compounds in corn and soybean crops over two years showed no significant difference between plots treated with and without MBS applications. For the same site, yields measured at harvest were similar between treatments. MBS application could thus represent a partial alternative to mineral fertilisers for field crops, while limiting the economic and environmental costs associated with their incineration and landfilling. It is also an economic advantage for agricultural producers given the possibility of using fewer mineral fertilisers and therefore reducing the environmental impact of their use.

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting.

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Irrigation with primary wastewater alters wood anatomy and composition in willow Salix miyabeana SX67.

Traditional treatment of wastewaters is a burden for local governments. Using short rotation coppice willow (SRCW) as vegetal filter has several environmental and economic benefits. Here, we investigated the effect of primary wastewater irrigation on wood structure and composition of the willow cultivar Salix miyabeana 'SX67' following two years of growth. Compared to unirrigated plants (UI), stem sections of plants irrigated with primary wastewater (WWD) showed an unexpected decrease of hydraulic conductance (KS) associated with a decrease in vessel density but not vessel diameter. The majority (86%) of vessels had diameters range groups [20-30[, [30-40[and [40-50[µm and contributed to > 75% of theoretical KS, while the group class [50-60[µm (less than 10% of vessels) still accounted for > 20% of total KS regardless irrigation treatments. WWD significantly alters the chemical composition of wood with an increase of glucan content by 9 to 16.4% and a decrease of extractives by 35.3 to 36.4% when compared to UI or to plants irrigated with potable water (PW). The fertigation did also increase the proportion of the tension wood which highly correlated with glucan content. In the context of energetic transition and mitigation of climate change, such results are of high interest since WWD effectively permit the phytofiltration of large amounts of organic contaminated effluents without impairing SRCW physiology.

Glyphosate has a negligible impact on bacterial diversity and dynamics during composting.

The herbicide glyphosate has several potential entry points into composting sites and its impact on composting processes has not yet been evaluated. To assess its impact on bacterial diversity and abundance as well as on community composition and dynamics, we conducted a mesocosm experiment at the Montreal Botanical Garden. Glyphosate had no effect on physicochemical property evolution during composting, while it was completely dissipated by the end of the experiment. Sampling at Days 0, 2, 28 and 112 of the process followed by 16S rRNA amplicon sequencing also found no effect of glyphosate on species richness and community composition. Differential abundance analyses revealed an increase of a few taxa in the presence of glyphosate, namely TRA3-20 (order Polyangiales), Pedosphaeraceae and BIrii41 (order Burkholderiales) after 28 days. In addition, five amplicon sequence variants (ASVs) had lower relative abundance in the glyphosate treatment compared to the control on Day 2, namely Comamonadaceae, Pseudomonas sp., Streptomyces sp., Thermoclostridium sp. and Actinomadura keratinilytica, while two ASVs were less abundant on Day 112, namely Pedomicrobium sp. and Pseudorhodoplanes sp. Most differences in abundance were measured between the different sampling points within each treatment. These results present glyphosate as a poor determinant of species recruitment during composting.

Treatment of Landfill Leachate by Short-Rotation Willow Coppice Plantations in a Large-Scale Experiment in Eastern Canada.

The treatment of leachate by vegetative filters composed of short-rotation willow coppice (SRWC) has been shown to be a cost-effective alternative to conventional and costly methods. However, few studies have considered the treatment capability of willow filters at a scale large enough to meet the industrial requirements of private landfill owners in North America. We report here on a field trial (0.5 ha) in which a willow plantation was irrigated with groundwater (D0) or aged leachate at two different loadings (D1 and D2, which was twice that of D1). Additionally, half of the D2-irrigated plots were amended with phosphorus (D2P). The system, which operated for 131 days, was highly efficient, causing the chemical oxygen demand concentration to drop significantly with the total removal of ammonia (seasonal average removal by a concentration of 99-100%). D2P efficacy was higher than that of D2, indicating that P increased the performance of the system. It also increased the willow biomass 2.5-fold compared to water irrigation. Leaf tissue analysis revealed significant differences in the concentrations of total nitrogen, boron, and zinc, according to the treatment applied, suggesting that the absorption capacity of willows was modified with leachate irrigation. These results indicate that the willow plantation can be effective for the treatment of landfill leachate in respect of environmental requirements.

Different Temperature and UV Patterns Modulate Berry Maturation and Volatile Compounds Accumulation in Vitis sp.

Volatile compounds (VCs) in grapevine berries play an important role in wine quality; however, such compounds and vine development can be sensitive to environmental conditions. Due to this sensitivity, changes in temperature patterns due to global warming are likely to further impact grape production and berry composition. The aim of this study was to determine the possible effects of different growing-degree day accumulation patterns on berry ripening and composition at harvest. An experimental field was conducted using Vitis sp. L'Acadie blanc, in Nova Scotia, Canada. Using on-the-row mini-greenhouses, moderate temperature increase and reduced ultraviolet (UV) exposure were triggered in grapevines during pre-veraison (inflorescence to the beginning of berry softening), post-veraison (berry softening to full maturity), and whole season (inflorescence to full maturity), while controls were left without treatment. Free and bound VCs were extracted from berries sampled at three different phenological stages between veraison and maturity before analysis by gas chromatography-mass spectrometry (GC-MS). Berries from grapevines exposed to higher temperatures during early berry development (pre-veraison and whole) accumulated significantly higher concentrations of benzene derivatives 2-phenylethanol and benzyl alcohol at harvest, but lower concentrations of hydroxy-methoxy-substituted volatile phenols, terpenes, and C13-norisoprenoids than the control berries. These results illustrate the importance of different environmental interactions in berry composition and suggest that temperature could potentially modulate phenylpropanoid and mevalonate metabolism in developing berries. This study provides insights into the relationships between abiotic conditions and secondary metabolism in grapevine and highlights the significance of early developmental stages on berry quality at harvest.

Microbial community origin and fate through a rural wastewater treatment plant.

Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterized. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge and post-treatment effluent were characterized. From 3163 exact sequence variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially human-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem.

Valuable alkaloids content is preserved in Camptotheca acuminata and Morus alba grown in trace elements contaminated soil.

Phytoextraction of trace elements (TE) using woody species is an economically challenging soil remediation approach because of the long time needed. Yet, some trees contain alkaloids that can be exploited along structural components to enhance biomass value. As alkaloids are thought to be involved in plant defence mechanisms, we hypothesized that potentially hostile phytoremediation conditions could increase their level. Camptothecin in Camptotheca acuminata and 1-deoxynojirimycin in Morus alba were measured from trees grown in a field in presence of Cu, Pb and Zn all together, and from M. alba grown in a greenhouse in presence of Cd or other abiotic stressors (NaCl and bending). The trees did not extract TE in the field, but M. alba stems accumulated Cd in the greenhouse experiment, with no consequence on stomatal conductance and leaves pigments concentration. Camptothecin and 1-deoxynojirimycin concentrations were preserved under all experimental conditions, as was biomass yield, and phenolics were slightly increased in M. alba exposed to TE. This study provides evidence that valuable and persistent alkaloids and phenolics can be extracted from trees facing phytoremediation-associated stresses, without a negative impact on their quantity and on biomass yield. Such products could generate a sustainable stream of revenues during phytoremediation.

There is scarce data on tree alkaloid content and scarcer data on how it is affected by exposure to trace elements in a phytoremediation context. We provide evidence that the content of two specific alkaloids is not altered in Morus alba and Camptotheca acuminata exposed to moderate to elevated levels of contaminating trace elements. The manuscript introduces the use of M. alba for phytoremediation in the Americas and is the first to propose the use of C. acuminata on trace element contaminated sites to produce camptothecin, a valuable anticancer alkaloid.

Dissipation and effect of glyphosate during composting of organic wastes.

The addition of organic matter (OM) containing glyphosate during compost production, through the introduction of contaminated plant residues or sewage sludge, presents a risk of hindering the proper OM breakdown carried out by microorganisms and causing the accumulation of glyphosate or aminomethylphosphonic acid (AMPA). To measure the effect of glyphosate and glyphosate-based herbicide (GBH) on OM decomposition as well as the dissipation of glyphosate to AMPA during composting, a controlled-environment experiment was conducted using mesocosm-scale vessels. Analytical-grade (AG) glyphosate (150 mg kg-1 ) and GBH (VisionMAX) equivalent to the amounts applied in agricultural areas (300 mg kg-1 ) were added to a mixture of green residues, which were then composted for 112 d. Sampling after 2, 7, 28, and 112 d showed a negligible effect of glyphosate and GBH on physicochemical properties of the mixture (temperature, OM%, pH, total carbon [C], total nitrogen [N], and C/N ratio), ammonification, nitrification, and phosphate content. No differences between AG glyphosate and GBH treatments were measured. Glyphosate levels decreased significantly after 2 d to reach 53.1 and 71.1% of the initial content for the AG glyphosate and GBH treatments, respectively, and glyphosate dissipation was almost complete after 112 d of composting. Aminomethylphosphonic acid could not be detected at any time during the experiment regardless of the treatment. Our results show that conditions for OM decomposition were maintained despite the addition of glyphosate and suggest that only trace amounts of glyphosate or AMPA are likely to be present in mature compost.

Willow and Herbaceous Species' Phytoremediation Potential in Zn-Contaminated Farm Field Soil in Eastern Québec, Canada: A Greenhouse Feasibility Study.

Phytoremediation shows great promise as a plant-based alternative to conventional clean-up methods that are prohibitively expensive. As part of an integrated strategy, the selection of well-adapted plant species as well as planting and management techniques could determine the success of a long-term program. Herein, we conducted an experiment under semi-controlled conditions to screen different plants species with respect to their ability to phytoremediate Zn-contaminated soil excavated from a contaminated site following a train derailment and spillage. The effect of nitrilotriacetic acid (NTA) application on the plants and soil was also comprehensively evaluated, albeit we did not find its use relevant for field application. In less than 100 days, substantial Zn removal occurred in the soil zone proximal to the roots of all the tested plant species. Three perennial herbaceous species were tested, namely, Festuca arundinacea, Medicago sativa, and a commercial mix purposely designed for revegetation; they all showed strong capacity for phytostabilization at the root level but not for phytoextraction. The Zn content in the aboveground biomass of willows was much higher. Furthermore, the degree of growth, physiological measurements, and the Zn extraction yield indicated Salix purpurea 'Fish Creek' could perform better than Salix miyabeana, 'SX67', in situ. Therefore, we suggest implementing an S. purpurea­perennial herbaceous co-cropping strategy at this decade-long-abandoned contaminated site or at similar disrupted landscapes.

Co-planting of Salix interior and Trifolium pratense for phytoremediation of trace elements from wood preservative contaminated soil.

Phytoextraction potential of a co-planting system was evaluated using a shrub and an herbaceous species and compared with monocultures. A greenhouse experiment with Salix interior and Trifolium pratense grown in combination or alone was conducted for 120 days in soil either uncontaminated or contaminated with wood preservatives containing mixed chromated copper arsenate and pentachlorophenol (PCP). The results showed that the plant species produced similar amounts of dry biomass per pot in monoculture and co-planting, whether growing in contaminated or uncontaminated soil. Arsenic (As), chromium (Cr) and copper (Cu) concentrations in root tissue of S. interior increased 8.6%, 65.9% and 4.5%, respectively, in co-planting compared to its monoculture. T. pratense had superior concentration of As (14% higher) in root tissue when co-planted. However, the higher trace elements concentrations in the plant tissues did not translate into measurable differences in total trace element removal per pot, except for As. The bioconcentration factor for Cu and As was high in the belowground portions of the plants in co-planting. PCP levels in the soil decreased to values near the limit of detection in all treatments. These results suggest that co-planting S. interior with T. pratense could lead to higher phytoextraction potential than monoculture.

A four-year phytoremediation trial to decontaminate soil polluted by wood preservatives: phytoextraction of arsenic, chromium, copper, dioxins and furans.

Widely used as wood preservatives for the last century, Pentachlorophenol (PCP) and chromated copper arsenate (CCA) have been shown to leach from treated surfaces and contaminate soil of wood storage sites. We performed a four-year field phytoremediation trial in southern Quebec (Canada) on a site contaminated with PCP and CCA with the following objectives: (1) assess the potential of willow, fescue, alfalfa and Indian mustard to tolerate and translocate CCA and PCP residues in their aerial tissues, (2) investigate the possibility of phytoextraction of dioxins and furans, and (3) test the effect of nitrogen fertilizer on phytoremediation performance. We showed that while nitrogen fertilization increased the chlorophyll content of plants, it did not result in a significantly greater plant biomass. We also showed that plants grown in the presence of PCP/CCA residues were able to translocate and concentrate trace elements in their aerial tissues, but also dioxins and furans (PCDD/F). This suggests that plants grown on sites polluted by PCP might contain dioxins and furans and should be treated as contaminated by these toxic chemicals. Finally, the reduction of soil contaminants at the end of the trial suggests that phytoremediation is a promising approach for decontaminating such sites.

Ectomycorrhizal Fungal Inoculation of Sphaerosporella brunnea Significantly Increased Stem Biomass of Salix miyabeana and Decreased Lead, Tin, and Zinc, Soil Concentrations during the Phytoremediation of an Industrial Landfill.

Fast growing, high biomass willows (Salix sp.) have been extensively used for the phytoremediation of trace element-contaminated environments, as they have an extensive root system and they tolerate abiotic stressors such as drought and metal toxicity. Being dual mycorrhizal plants, they can engage single or simultaneous symbiotic associations with both arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, which can improve overall plant health and growth. The aim of this study was to test the effect of these mycorrhizal fungi on the growth and trace element (TE) extraction potential of willows. A field experiment was carried out where we grew Salix miyabeana clone SX67 on the site of a decommissioned industrial landfill, and inoculated the shrubs with an AM fungus Rhizophagus irregularis, an EM fungus Sphaerosporella brunnea, or a mixture of both. After two growing seasons, the willows inoculated with the EM fungus S. brunnea produced significantly higher biomass. Ba, Cd and Zn were found to be phytoextracted to the aerial plant biomass, where Cd presented the highest bioconcentration factor values in all treatments. Additionally, the plots where the willows received the S. brunnea inoculation showed a significant decrease of Cu, Pb, and Sn soil concentrations. AM fungi inoculation and dual inoculation did not significantly influence biomass production and soil TE levels.

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments.

Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.

Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.

Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species-level microbial identification using paired-end sequences directly, multiple high-complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real-world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial.

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, ß, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome.

Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.

Complementarity of three distinctive phytoremediation crops for multiple-trace element contaminated soil.

Trace element (TE) contaminated land represents an important risk to the environment and to human health worldwide. These soils usually contain a variety of TEs which can be a challenge for plant-based remediation options. As individual plant species often possess a limited range of TE remediation abilities, functional complementarity principles could be of value for remediation of soil contaminated by multiple TEs using assemblages of species. Monocultures and polycultures of Festuca arundinacea, Medicago sativa and Salix miyabeana were grown for 4months in aged-polluted soil contaminated by Ag, As, Cd, Cr, Cu, Pb, Se and Zn. Above and belowground biomass yields, root surface area (RSA) and TE tissue concentrations were recorded. In monoculture, the greatest aboveground biomass was produced by S. miyabeana (S), the greatest belowground biomass was from M. sativa (M) and F. arundinacea (F) produced the highest RSA. The polycultures of F+M, F+S and F+M+S produced among the highest values across all three traits. F. arundinacea monoculture and its combination with S. miyabeana (F+S) accumulated the highest amounts of total TEs in belowground tissues, whereas the most effective combination (or monoculture) for aboveground extraction yields varied depending on the TE considered. The crops demonstrated complementarity in their biomass allocation patterns as well as facilitative interactions. When considering contamination with a particular TE, the best phytomanagement approach could include a specific monoculture option; however, when above and belowground biomass allocation patterns, TE-remediation abilities as well as nitrogen accessibility are considered, co-cropping all three species (F+M+S) was the most robust scenario for remediation of multiple-TE contaminated land. By more effectively addressing a diversity of TE, species assemblage approaches could represent an important advancement towards enabling the use of plants to address contaminated-land issues worldwide.