Genetic diversity of bacterial communities of serpentine soil and of rhizosphere of the nickel-hyperaccumulator plant Alyssum bertolonii

Soil microbial community structure and environmental effects of serpentine weathering under different vegetative covers in the serpentine mining area of Donghai County, China

The use of serpentine biological weathering to capture atmospheric CO₂ has attracted much attention. In the long-term mining activities in a serpentine mining area, a large amount of serpentine powder diffused into the surrounding forest and farmland soil. The study of the serpentine weathering in soils of different vegetative covers and the composition characteristics of soil carbonate has important implications for understanding the serpentine weathering and carbon sequestration under natural conditions. The microbial diversity on exposed rock serpentine surfaces and soil under different vegetative covers in the serpentine mining area in Donghai County, China was investigated by high-throughput sequencing technology, and the characteristics of serpentine weathering and soil carbonate in related area were also explored by XRF, XRD, SEM-EDS, and chemical analysis methods. The results showed that the richness and uniformity of the bacteria species community increased significantly with the increasing complexity of plant groups covering the rock surface, but the species richness and uniformity of fungi showed an overall declining trend. Furthermore, high‑magnesium calcite (HMC) is ubiquitous on the exposed rock surface and the soil under different vegetative covers in this area. Based on these results, combined with the verification test results of HMC fixed heavy metal ions, the model of serpentine weathering in serpentine mining soil to synthesize carbonate and fix heavy metal ions was developed. That is, with the increase in the degree of rock weathering and the colonization of plants, the soil and plants seem to shape jointly a relatively stable microbial community structure adapted to the environment of the serpentine mining area, which promotes the serpentine weathering coupled with the formation of HMC and immobilization of metal ions in the serpentine soil. This study provides a theoretical basis for the serpentine bio-weathering in the mine area to capture atmospheric CO₂.

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient

Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.

Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna

Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.

Risk management tools and the case study Brassica napus: evaluating possible effects of genetically modified plants on soil microbial diversity

The cultivation of GMPs in Europe raises many questions about the environmental risks, in particular about their ecological impact on non-target organisms and on soil properties. The aim of a multidisciplinary group engaged in a LIFE+project (MAN-GMP-ITA) was to validate and improve an existing environmental risk assessment (ERA) methodology on GMPs within the European legislative framework on GMOs. Given the impossibility of evaluating GMO impact directly, as GMPs are banned in Italy, GMPs have not been used at any stage of the project. The project thus specifically focused on the conditions for the implementation of ERA in different areas of Italy, with an emphasis on some sensitive and protected areas located in the North, Centre, and South of the country, in order to lay the necessary baseline for evaluating the possible effects of a GMP on soil communities. Our sub-group carried out soil analyses in order to obtain soil health and fertility indicators to be used as baselines in the ERA model. Using various methods of chemical, biochemical, functional and genetic analysis, our study assessed the changes in diversity and functionality of bacterial populations, and arbuscular mycorrhizal fungi. The results show that plant identity and growth, soil characteristics, and field site climatic parameters are key factors in contributing to variation in microbial community structure and diversity, thus validating our methodological approach. Our project has come to the conclusion that the uneven composition and biological-agronomical quality of soils need to be taken into consideration in a risk analysis within the framework of ERA for the release of genetically modified plants.

Rhizosphere effect and salinity competing to shape microbial communities in Phragmites australis (Cav.) Trin. ex-Steud

Rhizobacterial communities associated with Phragmites australis (Cav.) Trin. ex Steud. in a hypersaline pond close to Wuliangsuhai Lake (Inner Mongolia - China) were investigated and compared with the microbial communities in bulk sediments of the same pond. Microbiological analyses have been done by automated ribosomal intergenic spacer analysis (ARISA) and partial 16S rRNA gene 454 pyrosequencing. Although community richness was higher in the rhizosphere samples than in bulk sediments, the salinity seemed to be the major factor shaping the structure of the microbial communities. Halanaerobiales was the most abundant taxon found in all the different samples and Desulfosalsimonas was observed to be present more in the rhizosphere rather than in bulk sediment.

The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils

Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element - tolerating or - accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant-bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.

Fungal diversity is not determined by mineral and chemical differences in serpentine substrates

The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.

Isolation and characterization of metal resistant-tolerant rhizosphere bacteria from the serpentine soils in Turkey

Despite the number of studies describing metal hyper-accumulating plants and their associated bacteria in various regions and countries, there is no information on rhizosphere microbial potential of the Turkish serpentine soils. This study aimed to explore the rhizosphere microbial diversity of Ni-resistant, hyper-accumulating plants grown on Ni-rich soils and their metal tolerance-resistance characteristics. One hundred ninety-one locations were visited to collect soil and plant samples from different serpentine regions of Western Turkey. Following bioavailable and total Ni analysis of collected samples, the seeds of the selected plants with higher Ni content were taken to the growth/germination test in a range of serpentine soils in a growth chamber condition. In order to investigate the rhizosphere microbial diversity, Isatis pinnatiloba and Alyssum dasycarpum which were able to germinate and grow well in the preliminary tests, were introduced to 6-month greenhouse experiment in the range of three serpentine soils with higher bioavailable Ni content. I. pinnatiloba had a better stimulatory effect on the rhizosphere microbial diversity. A total of 22 bacterial isolates were identified from different soil conditions in the end of experiment. Following microbial identification and confirmation tests, 11 isolates were found to be resistant and tolerant to the increasing concentrations of Ni, Pb, Cd and Zn in the range of 50-2,000 mg L( - 1), which was considerably higher than those indicated by earlier studies. The strains isolated and identified from the Turkish serpentine soils were the members of genera Arthrobacter, Bacillus, Microbacterium and Staphylococcus.

Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils

In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.

Plant-by-plant variations of bacterial communities associated with leaves of the nickel hyperaccumulator Alyssum bertolonii Desv

Bacteria associated with tissues of metal-hyperaccumulating plants are of great interest due to the multiple roles they may play with respect to plant growth and resistance to heavy metals. The variability of bacterial communities associated with plant tissues of three populations of Alyssum bertolonii, a Ni hyperaccumulator endemic of serpentine outcrops of Central Italy, was investigated. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes was applied to DNA extracted from leaf tissues of 30 individual plants from three geographically separated serpentine outcrops. Moreover, T-RFLP fingerprinting was also performed on DNA extracted from the same soils from which the plants were collected. Fifty-nine unique terminal-restriction fragments (TRFs) were identified, with more than half of the taxonomically interpreted TRFs assigned to Alpha- and Gamma-Proteobacteria and Clostridia. Data were then used to define the extent of variation of bacterial communities due to single plants or to plant populations. Results indicated a very high plant-by-plant variation of leaf-associated community (more than 93% of total variance observed). However, a core (numerically small) of plant-specific TRFs was found. This work demonstrates that plant-associated bacterial communities represent a large reservoir of biodiversity and that the high variability existing between plants, even from the same population, should be taken into account in future studies on association between bacteria and metal-hyperaccumulating plants.

Biotechnological applications of serpentine soil bacteria for phytoremediation of trace metals

Serpentine or ultramafic soils are produced by weathering and pedogenesis of ultramafic rocks that are characterized by high levels of Ni, Cr, and sometimes Co, but contain low levels of essential nutrients such as N, P, K, and Ca. A number of plant species endemic to serpentine soils are capable of accumulating exceptionally high concentrations of Ni, Zn, and Co. These plants are known as metal "hyperaccumulators." The function of hyperaccumulation depends not only on the plant, but also on the interaction of the plant roots with rhizosphere microbes and the concentrations of bioavailable metals in the soil. The rhizosphere provides a complex and dynamic microenvironment where microorganisms, in association with roots, form unique communities that have considerable potential for the detoxification of hazardous materials. The rhizosphere bacteria play a significant role on plant growth in serpentine soils by various mechanisms, namely, fixation of atmospheric nitrogen, utilization of 1-aminocyclopropane-1-carboxylic acid (ACC) as the sole N source, production of siderophores, or production of plant growth regulators (hormones). Further, many microorganisms in serpentine soil are able to solubilize "unavailable" forms of heavy metal-bearing minerals by excreting organic acids. In addition, the metal-resistant serpentine isolates increase the efficiency of phytoextraction directly by enhancing the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass of hyperaccumulators. Hence, isolation of the indigenous and stress-adapted beneficial bacteria serve as a potential biotechnological tool for inoculation of plants for the successful restoration of metal-contaminated ecosystems. In this study, we highlight the diversity and beneficial features of serpentine bacteria and discuss their potential in phytoremediation of serpentine and anthropogenically metal-contaminated soils.

Rhizoremediation of metals: harnessing microbial communities

With the increasing successful stories of decontamination, different strategies for metal remediation are gaining importance and popularization in developing countries. Rhizoremediation, is one such promising option that harnesses the impressive capabilities of microorganisms associated with roots to degrade organic pollutants and transform toxic metals. Since it is a plant based in-situ phytorestoration technique it is proven to be economical, efficient and easy to implement under field conditions.Plants grown in metal contaminated sites harbor unique metal tolerant and resistant microbial communities in their rhizosphere. These rhizo-microflora secrete plant growth promoting substances, siderophores, phytochelators to alleviate metal toxicity, enhance the bioavailability of metals (phytoremediation) and complexation of metals (phytostabilisation). Selection of right bacteria/consortia and inoculation to seed/ roots of suitable plant species will widen the perspectives of rhizoremediation.

Isolation and characterization of endophytic bacteria from the nickel hyperaccumulator plant Alyssum bertolonii

We report the isolation and characterization of endophytic bacteria, endemic to serpentine outcrops of Central Italy, from a nickel hyperaccumulator plant, Alyssum bertolonii Desv. (Brassicaceae). Eighty-three endophytic bacteria were isolated from roots, stems, and leaves of A. bertolonii and classified by restriction analysis of 16S rDNA (ARDRA) and partial 16S rDNA sequencing in 23 different taxonomic groups. All isolates were then screened for siderophore production and for resistance to heavy metals. One isolate representative of each ARDRA group was then tested for plant tissue colonization ability in sterile culture. Obtained results pointed out that, despite the high concentration of heavy metals present in its tissues, A. bertolonii harbors an endophytic bacterial flora showing a high genetic diversity as well as a high level of resistance to heavy metals that could potentially help plant growth and Ni hyperaccumulation.

Superoxide dismutases of heavy metal resistant streptomycetes

Heavy metal tolerant and resistant strains of streptomycetes isolated from a former uranium mining site were screened for their superoxide dismutase expression. From the strains tolerating high concentrations of different heavy metals, one was selected for its tolerance of concentrations of heavy metals (Ni, Cu, Cd, Cr, Mn, Zn, Fe). This strain, Streptomyces acidiscabies E13, was chosen for the purpose of superoxide dismutase analysis. Gel electrophoresis and activity staining revealed only one each of a nickel (NiSOD) and an iron (FeZnSOD) containing superoxide dismutase as shown by differential enzymatic repression studies. The gene for nickel containing superoxide dismutase, sodN, was cloned and sequenced from this strain. The genomic sequence shows 92.7% nucleotide identity and 96.1% amino acid identity to sodN of S. coelicolor. Expression can be activated by nickel as well as other heavy metals and active enzyme is produced in media lacking nickel but containing copper, iron or zinc. Thus, the selected strain is well suited for further characterization of the enzyme encoded by sodN.

Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent

Transcripts of ribosomal RNA have been used for assessing the structure and dynamics of active bacterial populations; however, it remains unclear whether the information provided by community profiling derived from RNA is different from that derived from DNA, particularly when a selective pressure is applied on the bacterial community. In the present work, terminal-restriction fragment length polymorphism (T-RFLP) community profiles based on DNA and RNA extracted from soil microcosms treated with a toxic concentration of chromate were compared. Microcosms of a nonpolluted agricultural soil and of a heavy-metal-rich soil (serpentine) were treated with chromate and DNA and RNA were extracted. T-RFLP analysis was performed on amplified and retro-amplified 16SrRNA gene sequences, and band profiles obtained from samples of DNA and of RNA were compared. Some of the T-RFLP bands, identified as peculiar peaks in the profiles, were cloned and sequenced for taxonomic interpretation. Results indicated that: (1) community profiles derived from RNA and DNA were partly overlapping; (2) there was a strong correlation between the dynamics shown by RNA- and DNA-based T-RFLP profiles; (3) chromate addition exerted a clear effect on both agricultural and serpentine soil bacterial communities, either at the DNA and at the RNA level; however, the profiles derived from RNA showed sharper differences between treated and control samples than that of DNA-based profiles.