Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings

The Synergistic Impact of Arbuscular Mycorrhizal Fungi and Compost Tea to Enhance Bacterial Community and Improve Crop Productivity under Saline-Sodic Condition

Soil salinity has a negative impact on the biochemical properties of soil and on plant growth, particularly in arid and semi-arid regions. Using arbuscular mycorrhizal fungi (Glomus versiform) and foliar spray from compost tea as alleviating treatments, this study aimed to investigate the effects of alleviating salt stress on the growth and development of maize and wheat grown on a saline-sodic soil during the period of 2022/2023. Six treatments were used in the completely randomized factorial design experiment. The treatments included Arbuscular mycorrhizal fungus (AMF0, AMF1) and varied concentrations of compost tea (CT0, CT50, and CT100). AMF colonization, the bacterial community and endosphere in the rhizosphere, respiration rate, growth parameters, and the productivity were all evaluated. The application of AMF and CT, either separately or in combination, effectively mitigated the detrimental effects caused by soil salinity. The combination of AMF and CT proved to be highly efficient in improving the infection rate of AMF, the bacterial community in the rhizosphere and endosphere, growth parameters, and grain yield of maize and wheat. Therefore, it can be proposed that the inoculation of mycorrhizal fungi with compost tea in saline soils is an important strategy for enhancing salt tolerance in maize and wheat plants through improving microbial activity, the infection rate of AMF, and overall maize and wheat productivity.

Soil Mercury Pollution Changes Soil Arbuscular Mycorrhizal Fungal Community Composition

Remediation of mercury (Hg)-contaminated soil by mycorrhizal technology has drawn increasing attention because of its environmental friendliness. However, the lack of systematic investigations on arbuscular mycorrhizal fungi (AMF) community composition in Hg-polluted soil is an obstacle for AMF biotechnological applications. In this study, the AMF communities within rhizosphere soils from seven sites from three typical Hg mining areas were sequenced using an Illumina MiSeq platform. A total of 297 AMF operational taxonomic units (OTUs) were detected in the Hg mining area, of which Glomeraceae was the dominant family (66.96%, 175 OTUs). AMF diversity was significantly associated with soil total Hg content and water content in the Hg mining area. Soil total Hg showed a negative correlation with AMF richness and diversity. In addition, the soil properties including total nitrogen, available nitrogen, total potassium, total phosphorus, available phosphorus, and pH also affected AMF diversity. Paraglomeraceae was found to be negatively correlated to Hg stress. The wide distribution of Glomeraceae in Hg-contaminated soil makes it a potential candidate for mycorrhizal remediation.

Claroideoglomus etunicatum affects the structural and functional genes of the rhizosphere microbial community to help maize resist Cd and La stresses

Arbuscular mycorrhizal fungi (AMF) and plant rhizosphere microbes reportedly enhance plant tolerance to abiotic stresses and promote plant growth in contaminated soils. The co-contamination of soil by heavy metals (e.g., Cd) and rare earth elements (e.g., La) represents a severe environmental problem. Although the influence of AMF in the phytoremediation of contaminated soils is well documented, the underlying interactive mechanisms between AMF and rhizosphere microbes are still unclear. We conducted a greenhouse pot experiment to evaluate the effects of AMF (Claroideoglomus etunicatum) on maize growth, nutrient and metal uptake, rhizosphere microbial community, and functional genes in soils with separate and combined applications of Cd and La. The purpose of this experiment was to explore the mechanism of AMF affecting plant growth and metal uptake via interactions with rhizosphere microbes. We found that C. etunicatum (i) significantly enhanced plant nutritional level and biomass and decreased metal concentration in the co-contaminated soil; (ii) significantly altered the structure of maize rhizosphere bacterial and fungal communities; (iii) strongly enriched the abundance of carbohydrate metabolism genes, ammonia and nitrate production genes, IAA (indole-3-acetic acid) and ACC deaminase (1-aminocyclopropane-1-carboxylate) genes, and slightly altered the abundance of P-related functional genes; (iv) regulated the abundance of microbial quorum sensing system and metal membrane transporter genes, thereby improving the stability and adaptability of the rhizosphere microbial community. This study provides evidence of AMF improving plant growth and resistance to Cd and La stresses by regulating plant rhizosphere microbial communities and aids our understanding of the underlying mechanisms.

Effects of Antimony on Rice Growth and Its Existing Forms in Rice Under Arbuscular Mycorrhizal Fungi Environment

Arbuscular mycorrhizal fungi (AMF) can form symbiotic relationships with most terrestrial plants and regulate the uptake and distribution of antimony (Sb) in rice. The effect of AMF on the uptake and transport of Sb in rice was observed using pot experiments in the greenhouse. The results showed that AMF inoculation increased the contact area between roots and metals by forming mycelium, and changed the pH and Eh of the root soil, leading to more Sb entering various parts of the rice, especially at an Sb concentration of 1,200 mg/kg. The increase in metal toxicity further led to a decrease in the rice chlorophyll content, which directly resulted in a 22.7% decrease in aboveground biomass, 21.7% in underground biomass, and 11.3% in grain biomass. In addition, the antioxidant enzyme results showed that inoculation of AMF decreased 22.3% in superoxide dismutase, 9.9% in catalase, and 20.7% in peroxidase compared to the non-inoculation groups, further verifying the negative synergistic effect of AMF inoculation on the uptake of Sb in rice. The present study demonstrated the effect of AMF on the uptake and transport of Sb in the soil–rice system, facilitating future research on the related mechanism in the soil–rice system under Sb stress.

Sustainable and efficient stabilization/solidification of Pb, Cr, and Cd in lead-zinc tailings by using highly reactive pozzolanic solid waste

Lead-zinc tailings (LZTs) are industrial by-products containing a large number of heavy metals that seriously harm the ecological environment and human health. This study was performed to propose a sustainable and efficient method for immobilizing Pb, Cr, and Cd in LZTs by using solid waste. To better assess the immobilization performance and mechanism, the leaching toxicity, fraction distribution, unconfined compressive strength, environmental risk assessment, and hydration products were explored. The LZTs were mixed and molded with different constituents of ground granulated blast furnace slag (GGBFS) and rice husk ashes (RHAs) at different curing temperatures. Results suggest that ≥99% of the Pb, Cr, and Cd were immobilized mainly in the form of residual fractions in the LZTs. The amounts of Pb, Cr, and Cd in the bioavailable fractions notably decreased by approximately 99.83%, 99.58%, and 97.05%, respectively. After stabilization/solidification (S/S) disposal, Pb, Cr, and Cd showed low to even no risk. The RHAs were effective to stabilize Pb, and GGBFS was effective to stabilize Cr. However, both materials showed almost equal effects to Cd. Ettringite, C-S-H gel, and portlandite were the main hydration products to immobilize Pb, Cr, and Cd, and these hydration products provided a source of strength. Honey-comb or reticular network C-S-H gel possessed higher specific surface area, higher pore volume, and bigger pore size than the other materials. The proposed method could explain the sustainability and efficiency of the S/S of Pb, Cr, and Cd in LZTs by using RHAs. This study opens up new perspectives for disposing heavy metal by using accessible agricultural solid waste (i.e., RHAs) in rural areas, and the solidified block shows certain economic benefits.

Arbuscular Mycorrhizal Fungi Are an Influential Factor in Improving the Phytoremediation of Arsenic, Cadmium, Lead, and Chromium

The increasing expansion of mines, factories, and agricultural lands has caused many changes and pollution in soils and water of several parts of the world. In recent years, metal(loid)s are one of the most dangerous environmental pollutants, which directly and indirectly enters the food cycle of humans and animals, resulting in irreparable damage to their health and even causing their death. One of the most important missions of ecologists and environmental scientists is to find suitable solutions to reduce metal(loid)s pollution and prevent their spread and penetration in soil and groundwater. In recent years, phytoremediation was considered a cheap and effective solution to reducing metal(loid)s pollution in soil and water. Additionally, the effect of soil microorganisms on increasing phytoremediation was given special attention; therefore, this study attempted to investigate the role of arbuscular mycorrhizal fungus in the phytoremediation system and in reducing contamination by some metal(loid)s in order to put a straightforward path in front of other researchers.

Native soil amendments combined with commercial arbuscular mycorrhizal fungi increase biomass of Panicum amarum

Coastal dune restorations often fail because of poorly performing plants. The addition of beneficial microbes can improve plant performance, though it is unclear if the source of microbes matters. Here, we tested how native soil amendments and commercially available arbuscular mycorrhizal (AM) fungi influenced performance of Panicum amarum, a dominant grass on Texas coastal dunes. In a greenhouse experiment, we manipulated the identity of native soil amendments (from P. amarum, Uniola paniculata, or unvegetated areas), the presence of soil microbes in the native soil amendments (live or sterile), and the presence of the commercial AM fungi (present or absent). Native soils from vegetated areas contained 149% more AM fungal spores than unvegetated areas. The commercial AM fungi, when combined with previously vegetated native soils, increased aboveground biomass of P. amarum by 26%. Effects on belowground biomass were weaker, although the addition of any microbes decreased the root:shoot ratio. The origin of native soil amendments can influence restoration outcomes. In this case soil from areas with vegetation outperformed soil from areas without vegetation. Combining native soils with commercial AM fungi may provide a strategy for increasing plant performance while also maintaining other ecosystem functions provided by native microbes.

Effects of Aeration on the Formation of Arbuscular Mycorrhiza under a Flooded State and Copper Oxide Nanoparticle Removal in Vertical Flow Constructed Wetlands

In this study, six vertical flow constructed wetlands (VFCWs) planted with Phragmites australis were operated at different aeration times (4 h day^-1 and 8 h day^-1), aeration modes (continuous and intermittent), and arbuscular mycorrhizal fungi (AMF) inoculation treatments (inoculation with Rhizophagus intraradices and no inoculation) to explore the effects of different aeration strategies on the formation of arbuscular mycorrhiza under a flooded state in VFCWs. In addition, these VFCWs were further used to treat copper oxide nanoparticle (CuO-NP) wastewater to evaluate the correlations among aeration, colonization, growth, and CuO-NP removal. The highest AMF 28S copy number (1.99×10⁵) and colonization in reed roots, with values of 67%, 21%, and 1% for frequency (F%), intensity (M%), and arbuscule abundance (A%), were observed in the treatment with intermittent aeration for 4 h day^-1. Aeration significantly increased the dissolved oxygen (DO) concentration and AMF colonization in VFCWs, thereby promoting plant growth and the purification of the CuO-NPs. However, excessive and continuous aeration had little positive effect on AMF colonization. This study provides a theoretical basis for the application of AMF for improving pollutant removal performance in constructed wetlands.

Inoculation of Bacillus spp. Modulate the soil bacterial communities and available nutrients in the rhizosphere of vetiver plant irrigated with acid mine drainage

Acid mine drainage (AMD) is one of an important pollution sources associated with mining activities and often inhibits plant growth. Plant growth promoting bacteria has received extensive attention for enhancing adaptability of plants growing in AMD polluted soils. The present study investigated the effect of plant growth promoting Bacillus spp. (strains UM5, UM10, UM13, UM15 and UM20) to improve vetiver (Chrysopogon zizanioides L.) adaptability in a soil irrigated with 50% AMD. Bacillus spp. exhibited P-solubilization, IAA and siderophore production. The Bacillus spp. strains UM10 and UM13 significantly increased shoot (4.2-2.5%) and root (3.4-1.9%) biomass in normal and AMD-impacted soil, respectively. Bacillus sp. strain UM20 significantly increased soil AP (379.93 mg/kg) while strain UM13 increased TN (1501.69 mg/kg) and WEON (114.44 mg/kg) than control. Proteobacteria, Chloroflexi, Acidobacteria and Bacteroidetes are the dominant phyla, of which Acidobacteria (12%) and Bacteroidetes (8.5%) were dominated in soil inoculated with Bacillus sp. strain UM20 while Proteobacteria (70%) in AMD soil only. However, the Chao1 and evenness indices were significantly increased in soil inoculated with Bacillus sp. strain UM13. Soil pH, AP and N fractions were positively correlated with the inoculation of bacterial strains UM13 and UM20. Plant growth promoting Bacillus spp. strains UM13 and UM20 were the main contributors to the variations in the rhizosphere bacterial community structure, improving soil available P, TN, WEON, NO₃^--N thus could be a best option to promote C. zizanioides adaptability in AMD-impacted soils.

The arbuscular mycorrhizal fungus Rhizophagus intraradices and other microbial groups affect plant species in a copper-contaminated post-mining soil

BACKGROUND AND AIM

Arbuscular mycorrhizal fungi (AMF) have an important role in plant-microbe interactions. But, there are few studies in which the combined effect of AMF with a stress factor, such as the presence of a metal, on plant species were assessed. This study investigated the effect of arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices and other soil microbial groups in the presence of copper on three plant species in a microcosm experiment.

METHODS

Two grass species Poa compressa and Festuca rubra and one herb species Centaurea jacea were selected as model plants in a pot-design test in which soils were artificially contaminated with copper. Treatments were bacteria (control), saprophytic fungi, protists, and a combined treatment of saprophytic fungi and protists, all in the presence or absence of the AM fungal species. After sixty days, plants were harvested and the biomass of grass and herb species and microbial respiration were measured.

RESULTS

The results showed almost equal above- and belowground plant biomass and microbial respiration in the treatments in the presence or absence of R. intraradices. The herb species C. jecea responded significantly to the soil inoculation with AM fungus, while grass species showed inconsistent patterns. Significant effect of AMF and copper and their interactions was observed on plant biomass when comparing contaminated vs. non-contaminated soils.

CONCLUSION

Strong effect of AMF on the biomass of herb species and slight changes in plant growth with the presence of this fungal species in copper-spiked test soils indicates the importance of mycorrhizal fungi compared to other soil microorganisms in our experimental microcosms.

Arsenic and iron speciation and mobilization during phytostabilization of pyritic mine tailings

Particulate and dissolved metal(loid) release from mine tailings is of concern in (semi-) arid environments where tailings can remain barren of vegetation for decades and, therefore, become highly susceptible to dispersion by wind and water. Erosive weathering of metalliferous tailings can lead to arsenic contamination of adjacent ecosystems and increased risk to public health. Management via phytostabilization with the establishment of a vegetative cap using organic amendments to enhance plant growth has been employed to reduce both physical erosion and leaching. However, prior research suggests that addition of organic matter into the oxic weathering zone of sulfide tailings has the potential to promote the mobilization of arsenate. Therefore, the objective of the current work was to assess the impacts of phytostabilization on the molecular-scale mechanisms controlling arsenic speciation and lability. These impacts, which remain poorly understood, limit our ability to mitigate environmental and human health risks. Here we report on subsurface biogeochemical transformations of arsenic and iron from a three-year phytostabilization field study conducted at a Superfund site in Arizona, USA. Legacy pyritic tailings at this site contain up to 3 g kg^-1 arsenic originating from arsenopyrite that has undergone oxidation to form arsenate-ferrihydrite complexes in the top 1 m. Tailings were amended in the top 20 cm with 100, 150, or 200 g kg^-1 (300-600 T ha^-1) of composted organic matter and seeded with native halotolerant plant species. Treatments and an unamended control received irrigation of 360 ± 30 mm y^-1 in addition to 250 ± 160 mm y^-1 of precipitation. Cores to 1 m depth were collected annually for three years and sectioned into 20 cm increments for analysis by synchrotron iron and arsenic X-ray absorption spectroscopy (XAS) coupled with quantitative wet chemical and mass balance methods. Results revealed that > 80% of arsenic exists in ammonium oxalate-extractable and non-extractable phases, including dominantly ferrihydrite and jarosite. Arsenic release during arsenopyrite oxidation resulted in both downward translocation and As^(V) attenuation by stable Fe^(III)(oxyhydr)oxide and Fe^(III) (hydroxy)sulfate minerals over time, highlighting the need for sampling at multiple depths and time points for accurate interpretation of arsenic speciation, lability, and translocation in weathering profiles. Less than 1% of total arsenic was highly-labile, i.e. water-extractable, from all treatments, depths, and years, and more than 99% of arsenate released by arsenopyrite weathering was attenuated by association with secondary minerals. Although downward translocation of both arsenic and iron was detected during phytostabilization by temporal enrichment analysis, a similar trend was measured for the uncomposted control, indicating that organic amendment associated with phytostabilization practices did not significantly increase arsenic mobilization over non-amended controls.

Growth and lead uptake by Parkinsonia aculeata L. inoculated with Rhizophagus intraradices

The increased lead (Pb) pollution in the biosphere has resulted in serious environmental problems, so it is essential to evaluate phytoremediation strategies for contaminated soils. This study evaluated the growth and Pd absorption capacity of Pakinsonia aculeata, inoculated with an arbuscular mycorrhizal fungus (Rhizophagus intraradices) over 18 weeks under greenhouse conditions. Treatments included inoculated and non-inoculated plants combined with six Pb concentrations (0, 40, 80, 160, 320, 640 mg·L^-1) in the form of Pb(NO₃)₂. Results showed that mycorrhizal colonization in inoculated plants ranged from 5.0 to 6.7% and favored plant growth. Pb levels and AMF-inoculation had no effects on chlorophyll fluorescence values. AMF-plants absorbed significantly more Pb in roots (237.97 mg·kg^-1) than control plants (202.85 mg·kg^-1), as well as high translocation to shoots (27.02 mg·kg^-1) under the high Pb dose. The increase in Pb concentration reduced the P concentration in roots, and the P and N concentrations in shoots; however, the absorption and translocation of Ca and Mg was increased in shoots. Inoculation of R. intraradices improved both growth and Pb uptake of P. aculeata, under greenhouse conditions suggesting that this tree species may be potentially studied for detoxifying Pb-polluted soils.

New Soil, Old Plants, and Ubiquitous Microbes: Evaluating the Potential of Incipient Basaltic Soil to Support Native Plant Growth and Influence Belowground Soil Microbial Community Composition

The plant–microbe–soil nexus is critical in maintaining biogeochemical balance of the biosphere. However, soil loss and land degradation are occurring at alarmingly high rates, with soil loss exceeding soil formation rates. This necessitates evaluating marginal soils for their capacity to support and sustain plant growth. In a greenhouse study, we evaluated the capacity of marginal incipient basaltic parent material to support native plant growth and the associated variation in soil microbial community dynamics. Three plant species, native to the Southwestern Arizona-Sonora region, were tested with three soil treatments, including basaltic parent material, parent material amended with 20% compost, and potting soil. The parent material with and without compost supported 15%, 40%, and 70% germination of Common Bean (Phaseolus vulgaris L. ‘Tarahumara Norteño’), Mesquite (Prosopis pubescens Benth), and Panic Grass (Panicum Sonorum Beal), respectively, though germination was lower than in the potting soil. Plant growth was also sustained over the 30 day period, with plants in parent material (with and without amendment) reaching 50% height compared to those in the potting soil. A 16S rRNA gene amplicon sequencing approach showed Proteobacteria to be the most abundant phyla in both parent material and potting soil, followed by Actinobacteria. The potting soil showed Gammaproteobacteria (19.6%) to be the second most abundant class, but its abundance was reduced in the soil + plants treatment (5.6%–9.6%). Within the basalt soil type, Alphaproteobacteria (42.7%) and Actinobacteria (16.3%) had a higher abundance in the evaluated bean plant species. Microbial community composition had strong correlations with soil characteristics, but not plant attributes within a given soil material. Predictive functional potential capacity of the communities revealed chemoheterotrophy as the most abundant metabolism within the parent material, while photoheterotrophy and anoxygenic photoautotrophy were prevalent in the potting soil. These results show that marginal incipient basaltic soil, both with and without compost amendments, can support native plant species growth, and non-linear associations may exist between plant–marginal soil–microbial interactions.

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining

Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.

Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms

Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.

Initial microbial status modulates mycorrhizal inoculation effect on rhizosphere microbial communities

Arbuscular mycorrhizal fungi (AMF) play a central role in rhizosphere functioning as they interact with both plants and soil microbial communities. The conditions in which AMF modify plant physiology and microbial communities in the rhizosphere are still poorly understood. In the present study, four different plant species, (clover, alfalfa, ryegrass, tall fescue) were cultivated in either sterilized (γ ray) or non-sterilized soil and either inoculated with a commercial AMF (Glomus LPA Val 1.) or not. After 20 weeks of cultivation, the mycorrhizal rate and shoot and root biomasses were measured. The abundance and composition of bacteria, archaea, and fungi were analyzed, respectively, by quantitative PCR (qPCR) and fingerprinting techniques. Whilst sterilization did not change the AMF capacity to modify plant biomass, significant changes in microbial communities were observed, depending on the taxon and the associated plant. AMF inoculation decreases both bacterial and archaeal abundance and diversity, with a greatest extent in sterilized samples. These results also show that AMF exert different selections on soil microbial communities according to the plant species they are associated with. This study suggests that the initial abundance and diversity of rhizosphere microbial communities should be considered when introducing AMF to cultures.

Capability of the Invasive Tree Prosopis glandulosa Torr. to Remediate Soil Treated with Sewage Sludge

Sewage sludge improves agricultural soil and plant growth, but there are hazards associated with its use, including high metal(loid) contents. An experimental study was conducted under greenhouse conditions to examine the effects of sewage sludge on growth of the invasive tree Prosopis glandulosa, as well as to determine its phytoremediation capacity. Plants were established and grown for seven months along a gradient of sewage sludge content. Plant traits, soil properties, and plant and soil concentrations of N, P, K, Cd, Pb, Cu, Ni, Zn, Cr, Co, As, and Fe were recorded. The addition of sewage sludge led to a significant decrease in soil pH, and Ni, Co, and As concentrations, as well as an increase in soil organic matter and the concentrations of N, P, Cu, Zn, and Cr. Increasing sewage sludge content in the growth medium raised the total uptake of most metals by P. glandulosa plants due to higher biomass accumulation (taller plants with more leaves) and higher metal concentrations in the plant tissues. P. glandulosa concentrated more Cd, Pb, Cu, Zn, and Fe in its below-ground biomass (BGB) than in its above-ground biomass (AGB). P. glandulosa concentrated Ni, Co, and As in both BGB and AGB. P. glandulosa has potential as a biotool for the phytoremediation of sewage sludges and sewage-amended soils in arid and semi-arid environments, with a potential accumulation capability for As in plant leaves.

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.

Extreme Geochemical Conditions and Dispersal Limitation Retard Primary Succession of Microbial Communities in Gold Tailings

Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 10⁶ cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months' equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.

Arbuscular mycorrhizal inoculum sources influence bacterial, archaeal, and fungal communities' structures of historically dioxin/furan-contaminated soil but not the pollutant dissipation rate

Little is known about the influence of arbuscular mycorrhizal fungi (AMF) inoculum sources on phytoremediation efficiency. Therefore, the aim of this study was to compare the effects of two mycorrhizal inocula (indigenous and commercial inocula) in association with alfalfa and tall fescue on the plant growth, the bacterial, fungal, and archaeal communities, and on the removal of dioxin/furan (PCDD/F) from a historically polluted soil after 24 weeks of culture in microcosms. Our results showed that both mycorrhizal indigenous and commercial inocula were able to colonize plant roots, and the growth response depends on the AMF inoculum. Nevertheless, the improvement of root dry weight in inoculated alfalfa with indigenous inoculum and in inoculated tall fescue with commercial inoculum was clearly correlated with the highest mycorrhizal colonization of the roots in both plant species. The highest shoot dry weight was obtained in inoculated alfalfa and tall fescue with the commercial inoculum. AMF inoculation differently affected the number of bacterial and archaeal OTUs and bacterial diversity, with elevated bacterial and archaeal OTUs and bacterial diversity observed with indigenous inoculum. Mycorrhizal inoculation increases the abundance of bacterial OTUs (in particular with indigenous inoculum) and microbial richness but it does not improve PCDD/F dissipation. Vegetation had no effect on the abundance of microbial OTUs nor on richness but stimulated specific communities (Planctomycetia and Gammaproteobacteria) likely to be involved in the dissipation of PCDD/F. The reduction of toxic equivalency PCDD/F concentration also could be explained by the stimulation of soil microbial activities estimated with dehydrogenase and fluorescein diacetate hydrolase.

Beneficial Services of Arbuscular Mycorrhizal Fungi - From Ecology to Application

Arbuscular mycorrhiza (AM) is the most common symbiotic association of plants with microbes. AM fungi occur in the majority of natural habitats and they provide a range of important ecological services, in particular by improving plant nutrition, stress resistance and tolerance, soil structure and fertility. AM fungi also interact with most crop plants including cereals, vegetables, and fruit trees, therefore, they receive increasing attention for their potential use in sustainable agriculture. Basic research of the past decade has revealed the existence of a dedicated recognition and signaling pathway that is required for AM. Furthermore, recent evidence provided new insight into the exchange of nutritional benefits between the symbiotic partners. The great potential for application of AM has given rise to a thriving industry for AM-related products for agriculture, horticulture, and landscaping. Here, we discuss new developments in these fields, and we highlight future potential and limits toward the use of AM fungi for plant production.

Biochemical mechanism of phytoremediation process of lead and cadmium pollution with Mucor circinelloides and Trichoderma asperellum

This study focused on the bioremediation mechanisms of lead (0, 100, 500, 1000 mg kg^-1) and cadmium (0,10,50,100 mg kg^-1) contaminated soil using two indigenous fungi selected from mine tailings as the phytostimulation of Arabidopsis thaliana. The two fungal strains were characterized as Mucor circinelloides (MC) and Trichoderma asperellum (TA) by internal transcribed spacer sequencing at the genetic levels. Our research revealed that Cadmium was more toxic to plant growth than lead and meanwhile, MC and TA can strengthen A. thaliana tolerance to cadmium and lead with 40.19-117.50% higher root length and 58.31-154.14% shoot fresh weight of plant compared to non-inoculation. In this study, TA exhibited a higher potential to the inactivation of cadmium; however, MC was more effective in lead passivation. There was a direct correlation between the type of fungi, heavy metal content, heavy metal type and oxidative damage in plant. Both lead and cadmium induced oxidative damage as indicated by increased superoxide dismutase and catalase activities, while the antioxidant levels were significantly higher in fungal inoculated plants compared with those non-inoculated. The analysis of soil enzyme activity and taxonomic richness uncovered that the dominant structures of soil microbial community were altered by exogenous microbial agents. MC enhanced higher microbial diversity and soil enzyme activity than TA. The two indigenous fungi lessened several limiting factors with respect to phytoremediation technology, such as soil chemistry, contamination level and transformation, and metal solubility.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.

Effects of arbuscular mycorrhizal inoculation and biochar amendment on maize growth, cadmium uptake and soil cadmium speciation in Cd-contaminated soil

Experiments conducted to understand how arbuscular mycorrhizal (AM) inoculation or biochar application affect plant growth and heavy metal uptake have thus far looked at single applications of either soil amendment. There is little evidence of their synergistic effects, in particular for plants grown in cadmium (Cd) contaminated soil. We conducted a mesocosm experiment to investigate the effect of AM inoculation (Glomus intraradices BEG 141) and/or wheat-straw biochar amendment on maize (Zea mays L. cv. Hongdan No. 897) growth, antioxidant enzymatic activities, and Cd uptake, as well as soil Cd speciation under applications of 0, 3, 6 mg Cd per kg soil. Applying either AM inoculant or biochar alone significantly increased maize growth and reduced Cd uptake. Furthermore, solo AM inoculation alleviating Cd stress more fully than biochar, in turn facilitating maize growth and decreasing soil Cd translocation into plant tissue. Still, solo biochar amendment was more effective at inducing soil alkalinization and contributing to Cd immobilization. Adding biochar together with AM inoculant significantly promoted fungal populations compared to a control. Amending soil with AM inoculant and biochar together produced the largest increase in maize growth and decrease in tissue Cd concentrations. This effect was additive, with 79.1% greater biomass, 51.42%, 82.91%, 43.96% higher activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and 50.06%, 67.19%, 58.04% and 76.19% lower Cd concentrations in roots, stems, leaves, and ears, respectively, at a 6 mg kg^-1 Cd contamination rate. The combined treatment also had a synergistic effect on inducing soil alkalinization and causing Cd immobilization, and decreasing Cd phytoavailability and post-harvest transfer risks. These results suggest that AM inoculation in combination with biochar application may be applicable not only for maize production but also for phytostabilization of Cd-contaminated soil.

Influence of biochar and compost on phytoremediation of oil-contaminated soil

The use of pyrolyzed carbon, biochar, as a soil amendment is of potential interest for improving phytoremediation of soil that has been contaminated by petroleum hydrocarbons. To examine this question, the research reported here compared the effects of biochar, plants (mesquite tree seedlings), compost and combinations of these treatments on the rate of biodegradation of oil in a contaminated soil and the population size of oil-degrading bacteria. The presence of mesquite plants significantly enhanced oil degradation in all treatments except when biochar was used as the sole amendment without compost. The greatest extent of oil degradation was achieved in soil planted with mesquite and amended with compost (44% of the light hydrocarbon fraction). Most probable number assays showed that biochar generally reduced the population size of the oil-degrading community. The results of this study suggest that biochar addition to petroleum-contaminated soils does not improve the rate of bioremediation. In contrast, the use of plants and compost additions to soil are confirmed as important bioremediation technologies.

Assessment on cadmium and lead in soil based on a rhizosphere microbial community

The soil ecosystem is easily polluted by heavy metals. Cadmium (Cd) and lead (Pb), as the main pollutants of heavy metals, cause much harm to the soil ecosystem. However, the impact of the two chemicals on rhizosphere microorganisms remains almost unknown. The change of catalase (CAT) activity was consistent with the microbial biomass. 16S rRNA gene sequencing was performed on soil samples to study the toxic effect of heavy metals. On performing sequence analysis at the phylum and family taxonomic levels, 32 identified phyla and 303 families were observed. The dominant phylum was Proteobacteria followed by Bacteroidetes, Acidobacteria, and Actinobacteria. The relative abundance of the dominant phyla was obviously changed under the stress of Cd and Pb, suggesting that the heavy metal input had affected the microbial community structure. At the Order and Family levels, there was different variation of richness and diversity in Cd and Pb group as compared to those in the control group. Furthermore, abundance and similarity analysis showed the differences between Cd and Pb, indicating different toxicology effect on rhizosphere microbial communities because of the unique properties. This study provided a novel insight into the composition of microbial communities of rhizosphere, which could be used to evaluate the soil environment.

The influences of arbuscular mycorrhizal fungus on phytostabilization of lead/zinc tailings using four plant species

A greenhouse experiment was conducted to investigate the effects of the arbuscular mycorrhizal fungus Funneliformis mosseae on three parameters: Pb, Zn, Cu and Cd accumulation, translocation and plant growth in perennial ryegrass (Lolium perenne), tall fescue (Festuca arundinacea), showy stonecrop (Hylotelephium spectabile) and Purple Heart (Tradescantia pallida). The purpose of this work is to enhance site-specific phytostabilization of lead/zinc mine tailings using native plant species. The results showed that mycorrhizal fungi inoculation significantly increased plant biomass of F. arundinacea, H. spectabile and T. pallida. The Pb, Zn, Cu and Cd concentrations in roots were higher than those in shoots both with and without mycorrhizae, with the exception of the Zn concentration in H. spectabile. Mycorrhizae generally increased metal concentrations in roots and decreased metal concentrations in shoots of L. perenne and F. arundinacea. In addition, it was found that the majority of the bioconcentration and translocation factors were lower than 1 and mycorrhizal fungi inoculation further reduced these values. These results suggest that appropriate plant species inoculated with mycorrhiza might be a potential approach to revegetating mine tailing sites and that H. spectabile is an appropriate plant for phytostabilization of Pb/Zn tailings in northern China due to its higher biomass production and lower metal accumulation in shoots.

The Arbuscular Mycorrhizal Fungus Funneliformis mosseae Alters Bacterial Communities in Subtropical Forest Soils during Litter Decomposition

Bacterial communities and arbuscular mycorrhizal fungi (AMF) co-occur in the soil, however, the interaction between these two groups during litter decomposition remains largely unexplored. In order to investigate the effect of AMF on soil bacterial communities, we designed dual compartment microcosms, where AMF (Funneliformis mosseae) was allowed access (AM) to, or excluded (NM) from, a compartment containing forest soil and litterbags. Soil samples from this compartment were analyzed at 0, 90, 120, 150, and 180 days. For each sample, Illumina sequencing was used to assess any changes in the soil bacterial communities. We found that most of the obtained operational taxonomic units (OTUs) from both treatments belonged to the phylum of Proteobacteria, Acidobacteria, and Actinobacteria. The community composition of bacteria at phylum and class levels was slightly influenced by both time and AMF. In addition, time and AMF significantly affected bacterial genera (e.g., Candidatus Solibacter, Dyella, Phenylobacterium) involved in litter decomposition. Opposite to the bacterial community composition, we found that overall soil bacterial OTU richness and diversity are relatively stable and were not significantly influenced by either time or AMF inoculation. OTU richness at phylum and class levels also showed consistent results with overall bacterial OTU richness. Our study provides new insight into the influence of AMF on soil bacterial communities at the genus level.

Improvement of the soil nitrogen content and maize growth by earthworms and arbuscular mycorrhizal fungi in soils polluted by oxytetracycline

Interactions between earthworms (Eisenia fetida) and arbuscular mycorrhizal fungi (Rhizophagus intraradices, AM fungi) have been suggested to improve the maize nitrogen (N) content and biomass and were studied in soils polluted by oxytetracycline (OTC). Maize was planted and amended with AMF and/or earthworms (E) in the soil with low (1mgkg(-1) soil DM) or high (100mgkg(-1) soil DM) amounts of OTC pollution in comparison to soil without OTC. The root colonization, shoot and root biomass, shoot and root N contents, soil nitrogen forms, ammonia-oxidizing bacteria (AOB) and archaea (AOA) were measured at harvest. The results indicated that OTC decreased maize shoot and root biomass (p<0.05) by mediating the soil urease activity and AOB and AOA abundance, which resulted in a lower N availability for maize roots and shoots. There was a significant interaction between earthworms and AM fungi on the urease activity in soil polluted by OTC (p<0.05). Adding earthworms or AM fungi could increase the maize biomass and N content (p<0.05) in OTC polluted soil by increasing the urease activity and relieving the stress from OTC on the soil N cycle. AM fungi and earthworms interactively increased maize shoot and root biomass (p<0.05) in the OTC polluted soils through their regulation of the urease activity and the abundance of ammonia oxidizers, resulting in different soil NH4(+)-N and NO3(-)-N contents, which may contribute to the N content of maize shoots and roots. Earthworms and AM fungi could be used as an efficient method to relieve the OTC stress in agro-ecosystems.

Mine land valorization through energy maize production enhanced by the application of plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi

The use of heavy metals (HM) contaminated soils to grow energy crops can diminish the negative impact of HM in the environment improving land restoration. The effect of two PGPR (B1--Chryseobacterium humi ECP37(T) and B2--Pseudomonas reactans EDP28) and an AMF (F--Rhizophagus irregularis) on growth, Cd and Zn accumulation, and nutritional status of energy maize plants grown in a soil collected from an area adjacent to a Portuguese mine was assessed in a greenhouse experiment. Both bacterial strains, especially when co-inoculated with the AMF, acted as plant growth-promoting inoculants, increasing root and shoot biomass as well as shoot elongation. Cadmium was not detected in the maize tissues and a decrease in Zn accumulation was observed for all microbial treatments in aboveground and belowground tissues--with inoculation of maize with AMF and strain B2 leading to maximum reductions in Zn shoot and root accumulation of up to 48 and 43%, respectively. Although microbial single inoculation generally did not increase N and P levels in maize plants, co-inoculation of the PGPR and the AMF improved substantially P accumulation in roots. The DGGE analysis of the bacterial rhizosphere community showed that the samples inoculated with the AMF clustered apart of those without the AMF and the Shannon-Wiener Index (H') increased over the course of the experiment when both inoculants were present. This work shows the benefits of combined inoculation of AMF and PGPR for the growth energy maize in metal contaminated soils and their potential for the application in phytomanagement strategies.

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China

Arbuscular mycorrhizal fungi (AMF) have great potential for assisting heavy metal hyperaccumulators in the remediation of contaminated soils. However, little information is available about the community composition of AMF under natural conditions in soils contaminated by antimony (Sb). The objective of this study was to investigate the characteristics of AMF molecular diversity, and to explore the effects of Sb content and soil properties on the AMF community structure in an Sb mining area. Four Sb mine spoils and one adjacent reference area were selected from around the Xikuangshan mine in southern China. The association of AMF molecular diversity and community composition with the rhizosphere soils of the dominant plant species was studied by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results from all five studied sites showed that the diversity of AMF decreased with increasing Sb concentration. Principal component analysis (PCA) indicated that the AMF community structure was markedly different among these groups. Further redundancy analysis (RDA) showed that Sb contamination was the dominating factor influencing the AMF community structure in the Sb mine area. However, the multivariate analysis showed that, apart from the soil Sb content, extractable nitrogen content and organic matter content also attributed to AMF sequence distribution type. Some AMF sequences were only found in the highly contaminated area and these might be ideal candidates for improving phytoremediation efficiency in Sb mining regions. Gene sequencing analysis revealed that most species were affiliated with Glomus, suggesting that Glomus was the dominant AMF genus in the studied Sb mining area.

Abundance and Activity of 16S rRNA, AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings

Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings.

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.

Microbial inoculants and their impact on soil microbial communities: a review

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ

Caves are relatively accessible subterranean habitats ideal for the study of subsurface microbial dynamics and metabolisms under oligotrophic, non-photosynthetic conditions. A 454-pyrotag analysis of the V6 region of the 16S rRNA gene was used to systematically evaluate the bacterial diversity of ten cave surfaces within Kartchner Caverns, a limestone cave. Results showed an average of 1,994 operational taxonomic units (97 % cutoff) per speleothem and a broad taxonomic diversity that included 21 phyla and 12 candidate phyla. Comparative analysis of speleothems within a single room of the cave revealed three distinct bacterial taxonomic profiles dominated by either Actinobacteria, Proteobacteria, or Acidobacteria. A gradient in observed species richness along the sampling transect revealed that the communities with lower diversity corresponded to those dominated by Actinobacteria while the more diverse communities were those dominated by Proteobacteria. A 16S rRNA gene clone library from one of the Actinobacteria-dominated speleothems identified clones with 99 % identity to chemoautotrophs and previously characterized oligotrophs, providing insights into potential energy dynamics supporting these communities. The robust analysis conducted for this study demonstrated a rich bacterial diversity on speleothem surfaces. Further, it was shown that seemingly comparable speleothems supported divergent phylogenetic profiles suggesting that these communities are very sensitive to subtle variations in nutritional inputs and environmental factors typifying speleothem surfaces in Kartchner Caverns.

A greenhouse and field-based study to determine the accumulation of arsenic in common homegrown vegetables grown in mining-affected soils

The uptake of arsenic by plants from contaminated soils presents a health hazard that may affect home gardeners neighboring contaminated environments. A controlled greenhouse study was conducted in parallel with a co-created citizen science program (home garden experiment) to characterize the uptake of arsenic by common homegrown vegetables near the Iron King Mine and Humboldt Smelter Superfund site in southern Arizona. The greenhouse and home garden arsenic soil concentrations varied considerably, ranging from 2.35 to 533 mg kg(-1). In the greenhouse experiment four vegetables were grown in three different soil treatments and in the home garden experiment a total of 63 home garden produce samples were obtained from 19 properties neighboring the site. All vegetables accumulated arsenic in both the greenhouse and home garden experiments, ranging from 0.01 to 23.0 mg kg(-1) dry weight. Bioconcentration factors were determined and show that arsenic uptake decreased in the order: Asteraceae>Brassicaceae>Amaranthaceae>Cucurbitaceae>Liliaceae>Solanaceae>Fabaceae. Certain members of the Asteraceae and Brassicaceae plant families have been previously identified as hyperaccumulator plants, and it can be inferred that members of these families have genetic and physiological capacity to accumulate, translocate, and resist high amounts of metals. Additionally, a significant linear correlation was observed between the amount of arsenic that accumulated in the edible portion of the plant and the arsenic soil concentration for the Asteraceae, Brassicaceae, Amaranthaceae, and Fabaceae families. The results suggest that home gardeners neighboring mining operations or mine tailings with elevated arsenic levels should be made aware that arsenic can accumulate considerably in certain vegetables, and in particular, it is recommended that gardeners limit consumption of vegetables from the Asteraceae and Brassicaceae plant families.

A New Standard-Based Polynomial Interpolation (SBPIn) method to address gel-to-gel variability for the comparison of multiple denaturing gradient gel electrophoresis profile matrices

The Standard-Based Polynomial Interpolation (SBPIn) method is a new simple three-step protocol proposed to address common gel-to-gel variations for the comparison of sample profiles across multiple DGGE gels. The advantages of this method include no requirement for additional software or modification of the standard DGGE protocol.

Restoration of eroded soil in the Sonoran Desert with native leguminous trees using plant growth-promoting microorganisms and limited amounts of compost and water

Restoration of highly eroded desert land was attempted in the southern Sonoran Desert that had lost its natural capacity for self-revegetation. In six field experiments, the fields were planted with three native leguminous trees: mesquite amargo Prosopis articulata, and yellow and blue palo verde Parkinsonia microphylla and Parkinsonia florida. Restoration included inoculation with two of plant growth-promoting bacteria (PGPB; Azospirillum brasilense and Bacillus pumilus), native arbuscular mycorrhizal (AM) fungi, and small quantities of compost. Irrigation was applied, when necessary, to reach a rainy year (300 mm) of the area. The plots were maintained for 61 months. Survival of the trees was marginally affected by all supplements after 30 months, in the range of 60-90%. This variation depended on the plant species, where all young trees were established after 3 months. Plant density was a crucial variable and, in general, low plant density enhanced survival. High planting density was detrimental. Survival significantly declined in trees 61 months after planting. No general response of the trees to plant growth-promoting microorganisms and compost was found. Mesquite amargo and yellow palo verde responded well (height, number of branches, and diameter of the main stem) to inoculation with PGPB, AM fungi, and compost supplementation after three months of application. Fewer positive effects were recorded after 30 months. Blue palo verde did not respond to most treatments and had the lowest survival. Specific plant growth parameters were affected to varying degrees to inoculations or amendments, primarily depending on the tree species. Some combinations of tree/inoculant/amendment resulted in small negative effects or no response when measured after extended periods of time. Using native leguminous trees, this study demonstrated that restoration of severely eroded desert lands was possible.

Poplar clones of different sizes, grown on a heavy metal polluted site, are associated with microbial populations of varying composition

We performed a field trial to evaluate the response of different poplar clones to heavy metals. We found that poplar plants of the same clone, propagated by cuttings, had a marked variability of survival and growth in different zones of the field that were characterized by very similar physical-chemical prosperities. Since metal uptake and its accumulation by plants can be affected by soil microorganisms, we investigated soil microbial populations that were collected in proximity to the roots of large and small poplar plants. We used microbiological and molecular tools to ascertain whether bacterial strains or species were associated with large, or small poplars, and whether these were different from those present in the bulk (without plants) soil. We found that the culturable fraction of the bacteria differed in the three cases (bulk soil, small or large poplars). While some taxa were always present, two species (Chryseobacterium soldanellicola and Variovorax paradoxus) were only found in the soil where poplars (large or small) were growing, independently from the plant size. Bacterial strains of the genus Flavobacterium were prevalent in the soil with large poplar plants. The existence of different microbial populations in the bulk and in the poplar grown soils was confirmed by the DGGE profiles of the bacterial culturable fractions. Cluster analysis of the DGGE profiles highlighted the clear separation of the culturable fraction from the whole microbial community. The isolation and identification of poplar-associated bacterial strains from the culturable fraction of the microbial community provided the basis for further studies aimed at the combined use of plants and soil microorganisms in the remediation of heavy metal polluted soils.

Response of key soil parameters during compost-assisted phytostabilization in extremely acidic tailings: effect of plant species

Phytostabilization of mine tailings acts to mitigate both eolian dispersion and water erosion events which can disseminate barren tailings over large distances. This technology uses plants to establish a vegetative cover to permanently immobilize contaminants in the rooting zone, often requiring addition of an amendment to assist plant growth. Here we report the results of a greenhouse study that evaluated the ability of six native plant species to grow in extremely acidic (pH ∼ 2.5) metalliferous (As, Pb, Zn: 2000-3000 mg kg(-1)) mine tailings from Iron King Mine Humboldt Smelter Superfund site when amended with a range of compost concentrations. Results revealed that three of the six plant species tested (buffalo grass, mesquite, and catclaw acacia) are good candidates for phytostabilization at an optimum level of 15% compost (w/w) amendment showing good growth and minimal shoot accumulation of metal(loid)s. A fourth candidate, quailbush, also met all criteria except for exceeding the domestic animal toxicity limit for shoot accumulation of zinc. A key finding of this study was that the plant species that grew most successfully on these tailings significantly influenced key tailings parameters; direct correlations between plant biomass and both increased tailings pH and neutrophilic heterotrophic bacterial counts were observed. We also observed decreased iron oxidizer counts and decreased bioavailability of metal(loid)s mainly as a result of compost amendment. Taken together, these results suggest that the phytostabilization process reduced tailings toxicity as well as the potential for metal(loid) mobilization. This study provides practical information on plant and tailings characteristics that is critically needed for successful implementation of assisted phytostabilization on acidic, metalliferous mine tailings sites.