Microbially supported phytoremediation of heavy metal contaminated soils: strategies and applications

Isolation and screening of phosphorus solubilizing bacteria from saline alkali soil and their potential for Pb pollution remediation

The high pH and salinity of saline alkali soil not only seriously restrict the growth of crops, but also aggravate the pollution of heavy metals. The fixation of heavy metals and the regulation of pH by phosphorus solubilizing microorganisms may become a new way to repair heavy mental and improve saline alkali soil. In this study, a saline-alkali resistant bacteria (CZ-B1, CGMCC No: 1.19458) was screened from saline-alkali soil, and its tolerance to salt/alkali/lead stress was investigated by shaking flask experiment. The strain was identified as Bacillus amyloliquefaciens by morphology and 16S rRNA gene sequence analysis. The optimum growth temperature of CZ-B1 is about 35°C-40℃. The maximum salt stress and pH that it can tolerance are 100 g/L and 9 respectively, and its tolerance to Pb²⁺ can reach 2000 mg/L. The phosphorus release amount of CZ-B1 to Ca₃(PO₄)₂ within 72 h is 91.00-102.73 mg/L. The phosphate solubilizing index in PVK agar medium and NBRIP agar medium are more than 2, which can be defined as phosphate solubilizing bacteria. Moreover, the dissolution of CZ-B1 to phosphorus is mainly attributed to tartaric acid, citric acid and succinic acid in inorganic medium. In addition, the removal rate of Pb²⁺ by CZ-B1 can reach 90.38% for 500 mg/L. This study found that CZ-B1 can immobilize Pb through three biological mechanisms (organic acid, extracellular polymers and mineralization reaction). The release of succinic acid (10.97 g/L) and citric acid (5.26 g/L) may be the main mechanism to promote the mineralization reaction of CZ-B1 (phosphate and oxalate) and resistance to Pb stress. In addition, the high enrichment of Pb²⁺ by EPS can increase the rate of extracellular electron transfer and accelerate the mineralization of CZ-B1. The screening and domestication of saline-tolerant phosphorus-solubilizing bacteria not only help to remediate Pb contamination in saline soils, but also can provide P element for plant growth in saline soil.

Biomineralization by Extremely Halophilic and Metal-Tolerant Community Members from a Sulfate-Dominated Metal-Rich Environment

The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters and sediment soils were screened for isolates surviving high salt and metal concentrations. The high salt contents consisted mainly of chloride and sulfate, both in soil and riverbed sediment samples, accompanied by high metal loads with presence of cesium and strontium. The community structure was dominated by Chloroflexi, Proteobacteria and Acidobacteriota, while only at the highest contaminations did Firmicutes and Desulfobacterota reach appreciable percentages in the DNA-based community analysis. The extreme conditions providing high stress were mirrored by low numbers of cultivable strains. Thirty-four extremely halotolerant bacteria (23 Bacillus sp. and another 4 Bacillales, 5 Actinobacteria, and 1 Gamma-Proteobacterium) surviving 25 to 100 mM SrCl₂, CsCl, and Cs₂SO₄ were further analyzed. Mineral formation of strontium- or cesium-struvite could be observed, reducing bioavailability and thereby constituting the dominant metal and salt resistance strategy in this environment.

Optimization of Growth Conditions of Acinetobacter sp. Cr1 for Removal of Heavy Metal Cr Using Central Composite Design

Growth conditions can significantly affect the removal efficiency of heavy metals by microorganisms. The goal of this study was enhancing the removal efficiency of Cr(VI) and improving the application of Acinetobacter sp. Cr1 (GenBank accession number of 16S rDNA sequence, MN900681). This study focused on pH, Cr(VI) concentration and culture time, which were the major influence factors for removal efficiency of Cr(VI). A central composite design was employed to optimize the removal efficiency by optimizing three variables. The optimum growth conditions were as: pH of 9.52, Cr(VI) concentration of 128.55 mg l^-1, culture time of 43.30 h, and the predicted and actual maxima were 65.13% and 67.26%, respectively. Therefore, it is suggested that the strain Acinetobacter sp. Cr1 had a promising potential to be used for bioremediation of Cr(VI).

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities

The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms–both pathogenic and beneficial–have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.

Degradation of ferrocyanide by natural isolated bacteria

This study aims at investigating the iron cyanide (CN) degradation potential of two natural bacterial isolates with the purpose of their application in iron CN phytoremediation. The strains were isolated from contaminated soil and incubated over 4 months with 50 mg L^-1 CN (as ferrocyanide) as the sole iron and nitrogen source. Unlike previous reports, the study provides control for bacterial growth, biotic and abiotic CN losses. Bacterial growth, CN, ammonium, and nitrate concentrations were monitored regularly. Both strains grew less rapid with iron CN compared with the positive control. However, the growth was diauxic. The CN concentration in the media decreased with 20% and 25% respectively, while that in the sterile controls remained stable. Ammonium was detected in the media of both strains implying that a fraction of the initially applied ferrocyanide has been converted. The nitrogen lost from the system evened out with that in the cells at the end of the experiments. These results showed that the investigated strains were undoubtedly able to grow on iron CN as an alternative nitrogen source, but contrary to some previous findings, the iron CN utilization is much slower and takes place only after complete exhaustion of the cellular nitrogen reserves.

Characterization of the Tibet plateau Jerusalem artichoke (Helianthus tuberosus L.) transcriptome by de novo assembly to discover genes associated with fructan synthesis and SSR analysis

BACKGROUND

Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers and represent the foundation for their formation, processing and utilization of yield; and are also widely used in new sugar-based materials, bioenergy processing, ecological management, and functional feed. To identify key genes in the metabolic pathway of fructans in Jerusalem artichoke, high-throughput sequencing was performed using Illumina Hi Seq™ 2500 equipment to construct a transcriptome library.

RESULTS

Qinghai-Tibet Plateau Jerusalem artichoke "Qingyu No.1" was used as the material; roots, stems, leaves, flowers and tubers of Jerusalem artichoke in its flowering stage were mixed into a mosaic of the Jerusalem artichoke transcriptome library, obtaining 63,089 unigenes with an average length of 713.6 bp. Gene annotation through the Nr, Swiss Prot, GO, KOG and KEGG databases revealed 34.95 and 46.91% of these unigenes had similar sequences in the Nr and Swiss Prot databases. The GO classification showed the Jerusalem artichoke unigenes were divided into three ontologies, with a total of 49 functional groups encompassing biological processes, cellular components, and molecular functions. Among them, there were more unigenes involved in the functional groups for cellular processes, metabolic processes, and single-organism processes. 38,999 unigenes were annotated by KOG and divided into 25 categories according to their functions; the most common annotation being general function prediction. A total of 13,878 unigenes (22%) were annotated in the KEGG database, with the largest proportion corresponding to pathways related to carbohydrate metabolism. A total of 12 unigenes were involved in the synthesis and degradation of fructan. Cluster analysis revealed the candidate 12 unigene proteins were dispersed in the 5 major families of proteins involved in fructan synthesis and degradation. The synergistic effect of INV gene is necessary during fructose synthesis and degradation in Jerusalem artichoke tuber development. The sequencing data from the transcriptome of this species can provide a reliable data basis for the identification and assessment of the expression of the members of the INV gene family.A simple sequence repeat (SSR) loci search was performed on the transcriptome data of Jerusalem artichoke, identifying 6635 eligible SSR loci with a large proportion of dinucleotide and trinucleotide repeats, and the most different motifs were repeated 5 times and 6 times. Dinucleotide and trinucleotide repeat motifs were the most frequent, with AG/CT and ACC/GGT repeat motifs accounting for the highest proportion.

CONCLUSIONS

In this study, a database search of the transcriptome of the Jerusalem artichoke from the Qinghai Tibet Plateau was conducted by high throughput sequencing technology to obtain important transcriptional and SSR loci information. This allowed characterization of the overall expression features of the Jerusalem artichoke transcriptome, identifying the key genes involved in metabolism in this species. In turn, this offers a foundation for further research on the regulatory mechanisms of fructan metabolism in Jerusalem artichoke.

Functions of the C2H2 Transcription Factor Gene thmea1 in Trichoderma harzianum under Copper Stress Based on Transcriptome Analysis

Trichoderma spp. are important biocontrol filamentous fungi and have tremendous potential in soil bioremediation. In our previous studies, a C2H2 type transcription factor coding gene (thmea1) was cloned from a biocontrol agent T. harzianum Th-33; the encoded sequence of thmea1 contained 3 conserved C2H2 domains with Swi5 and Ace2 in Saccharomyces cerevisiae. The thmea1 knockout mutant Δthmea1 showed 12.9% higher copper tolerance than the wild-type Th33. To elucidate the function of thmea1 and its relationship with copper stress response, we conducted transcriptome sequencing and analysis of wild-type Th33 and Δthmea1 under 0.8 mM copper stress. A total of 1061 differentially expressed genes (DEGs) were identified between the two strains, all DEGs were assigned to KEGG pathway database, 383 DEGs were annotated in 191 individual pathways, and the categories of ribosomal protein synthesis and amino acid metabolism were the most highly enriched ones. Analysis of related DEGs showed that the expression levels of intracellular glutathione detoxification enzyme, heat shock proteins, and ribosomal proteins in Δthmea1 were higher than that of the wild-type Th33, and the expression of metallothionein (MT) gene did not change. In addition, the expression levels of genes coding for proteins associated with the Ccc2p-mediated copper chaperone Atx1p transport of copper ions into the Golgi secretory pathway increased, as well as the copper amine oxidase (CuAO). These findings suggest that Thmea1 is a negative regulated factor of copper tolerance ability in T. harzianum. It does not show metallothionein expression activator activities as that of Ace2 in S. cerevisiae. We hypothesize that after T. harzianum has lost its thmea1 gene, the ability of cells to scavenge reactive oxygen species, mainly through the glutathione antioxidant system, is enhanced, whereas protein synthesis and repair and copper secretion increase under copper stress, which increases the ability of the mutant strain to tolerate copper stress.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies.IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria.

Phytolacca acinosa Roxb. with Arthrobacter echigonensis MN1405 enhances heavy metal phytoremediation

The growth and metal-extraction efficiency of plants when exposed to toxic metals can be enhanced by inoculating with certain bacteria, but the mechanisms of this process remain unclear. We report results from glasshouse experiments on the effect of Arthrobacter echigonensis MN1405 in promoting Phytolacca acinosa Roxb. growth when exposed to 100 mg/L Mn solution. Mn removal efficiency in solution was significantly enhanced by bacterial inoculation; Mn was accumulated in the root of P. acinosa Roxb. plant. The bacteria oxidized the Mn on root surface, which formed a Mn plaque to serve as a barrier or a containment to prevent metal toxicity. In this process, pH condition was an important factor on the effects of microbial-assisted heavy metal phytoremediation. Our finding suggests that A. echigonensis MN1405 assisted P. acinosa to achieve high remediation efficiency of Mn removal and accumulation in Mn contamination area.

Screening beneficial rhizobacteria from Spartina maritima for phytoremediation of metal polluted salt marshes: comparison of gram-positive and gram-negative strains

The aim of our work was the isolation and characterization of bacteria from the rhizosphere of Spartina maritima in the metal contaminated Odiel estuary (Huelva, SW Spain). From 25 strains, 84 % were identified as gram-positive, particularly Staphylococcus and Bacillus. Gram-negative bacteria were represented by Pantoea and Salmonella. Salt and heavy metal tolerance, metal bioabsorption, plant growth promoting (PGP) properties, and biofilm formation were investigated in the bacterial collection. Despite the higher abundance of gram-positive bacteria, gram-negative isolates displayed higher tolerance toward metal(loid)s (As, Cu, Zn, and Pb) and greater metal biosorption, as deduced from ICP-OES and SEM-EDX analyses. Besides, they exhibited better PGP properties, which were retained in the presence of metals and the ability to form biofilms. Gram-negative strains Pantoea agglomerans RSO6 and RSO7, together with gram-positive Bacillus aryabhattai RSO25, were selected for a bacterial consortium aimed to inoculate S. maritima plants in metal polluted estuaries for phytoremediation purposes.

Endophytic Cultivable Bacteria of the Metal Bioaccumulator Spartina maritima Improve Plant Growth but Not Metal Uptake in Polluted Marshes Soils

Endophytic bacterial population was isolated from Spartina maritima tissues, a heavy metal bioaccumulator cordgrass growing in the estuaries of Tinto, Odiel, and Piedras River (south west Spain), one of the most polluted areas in the world. Strains were identified and ability to tolerate salt and heavy metals along with plant growth promoting and enzymatic properties were analyzed. A high proportion of these bacteria were resistant toward one or several heavy metals and metalloids including As, Cu, and Zn, the most abundant in plant tissues and soil. These strains also exhibited multiple enzymatic properties as amylase, cellulase, chitinase, protease and lipase, as well as plant growth promoting properties, including nitrogen fixation, phosphates solubilization, and production of indole-3-acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The best performing strains (Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18, and Salinicola peritrichatus SMJ30) were selected and tested as a consortium by inoculating S. maritima wild plantlets in greenhouse conditions along with wild polluted soil. After 30 days, bacterial inoculation improved plant photosynthetic traits and favored intrinsic water use efficiency. However, far from stimulating plant metal uptake, endophytic inoculation lessened metal accumulation in above and belowground tissues. These results suggest that inoculation of S. maritima with indigenous metal-resistant endophytes could mean a useful approach in order to accelerate both adaption and growth of this indigenous cordgrass in polluted estuaries in restorative operations, but may not be suitable for rhizoaccumulation purposes.

Siderophore production by streptomycetes-stability and alteration of ferrihydroxamates in heavy metal-contaminated soil

Heavy metal-contaminated soil derived from a former uranium mining site in Ronneburg, Germany, was used for sterile mesocosms inoculated with the extremely metal-resistant Streptomyces mirabilis P16B-1 or the sensitive control strain Streptomyces lividans TK24. The production and fate of bacterial hydroxamate siderophores in soil was analyzed, and the presence of ferrioxamines E, B, D, and G was shown. While total ferrioxamine concentrations decreased in water-treated controls after 30 days of incubation, the sustained production by the bacteria was seen. For the individual molecules, alteration between neutral and cationic forms and linearization of hydroxamates was observed for the first time. Mesocosms inoculated with biomass of either strain showed changes of siderophore contents compared with the non-treated control indicating for auto-alteration and consumption, respectively, depending on the vital bacteria present. Heat stability and structural consistency of siderophores obtained from sterile culture filtrate were shown. In addition, low recovery (32 %) from soil was shown, indicating adsorption to soil particles or soil organic matter. Fate and behavior of hydroxamate siderophores in metal-contaminated soils may affect soil properties as well as conditions for its inhabiting (micro)organisms.

Microbially assisted phytoremediation approaches for two multi-element contaminated sites

Phytoremediation is an environmental friendly, cost-effective technology for a soft restoration of abandoned mine sites. The grasses Agrostis capillaris, Deschampsia flexuosa and Festuca rubra, and the annual herb Helianthus annuus were combined with microbial consortia in pot experiments on multi-metal polluted substrates collected at a former uranium mine near Ronneburg, Germany, and a historic copper mine in Kopparberg, Sweden, to test for phytoextraction versus phytostabilization abilities. Metal uptake into plant biomass was evaluated to identify optimal plant-microbe combinations for each substrate. Metal bioavailability was found to be plant species and element specific, and influenced by the applied bacterial consortia of 10 strains, each isolated from the same soil to which it was applied. H. annuus showed high extraction capacity for several metals on the German soil independent of inoculation. Our study could also show a significant enhancement of extraction for F. rubra and A. capillaris when combined with the bacterial consortium, although usually grasses are considered metal excluder species. On the Swedish mixed substrate, due to its toxicity, with 30 % bark compost, A. capillaris inoculated with the respective consortium was able to extract multi-metal contaminants.