Intimate communication between Comamonas aquatica and Fusarium solani in remediation of heavy metal-polluted environments

Evaluation of physiochemical, heavy metals, and bacteriological parameters of celery and its irrigation water within Sulaymaniyah city of Iraq

This study rigorously assesses the physicochemical, heavy metal concentrations, and bacteriological parameters of celery and its irrigation water across three rural areas of Sulaymaniyah city, Iraq. The investigation revealed that irrigation water's pH ranged significantly from 6.9 to 8.9. Notably, phosphate concentrations (PO43-) exceeded permissible levels in Tanjaro and Kanaswra across all seasons, with the highest recorded concentration being 10.4 mg L-1 during autumn in Kanaswra. Conversely, sulfate (SO42-) and sodium (Na+) concentrations remained within standard limits, with SO42- peaking at 115.1 mg L-1 in Tanjaro during summer. Celery samples reflected high Na+ concentrations in some seasons, with values exceeding 570 mg·kg in Kanaswra during summer. Heavy metal analysis indicated remarkably low levels in irrigation water, yet celery samples from Tanjaro and Aziz Awa exhibited Pb concentrations above the safety threshold of 0.3 mg·kg in all seasons. Furthermore, bacterial contamination, including total aerobic count and coliform in both water and celery, surpassed standard limits, highlighting significant health risks. This study underscores the imperative need for stringent water treatment processes to mitigate contamination and safeguard agricultural productivity and human health.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

Microbial interactions within beneficial consortia promote soil health

By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.

Aeromonas sobria as a potential candidate for bioremediation of heavy metal from contaminated environments

The uncontrolled discharge of industrial wastes causes the accumulation of high heavy metal concentrations in soil and water, leading to many health issues. In the present study, a Gram-negative Aeromonas sobria was isolated from heavily contaminated soil in the Tanjaro area, southwest of Sulaymaniyah city in the Kurdistan Region of Iraq; then, we assessed its ability to uptake heavy metals. A. sobria was molecularly identified based on the partial amplification of 16S rRNA using novel primers. The sequence was aligned with 33 strains to analyze phylogenetic relationships by maximum likelihood. Based on maximum tolerance concentration (MTC), A. sobria could withstand Zn, Cu, and Ni at concentrations of 5, 6, and 8 mM, respectively. ICP-OES data confirmed that A. sobria reduced 54.89% (0.549 mM) of the Cu, 62.33% (0.623 mM) of the Ni, and 36.41% (0.364 mM) of the Zn after 72 h in the culture medium. Transmission electron microscopy (TEM) showed that A. sobria accumulated both Cu and Ni, whereas biosorption was suggested for the Zn. These findings suggest that metal-resistant A. sobria could be a promising candidate for heavy metal bioremediation in polluted areas. However, more broadly, research is required to assess the feasibility of exploiting A. sobria in situ.

Heavy Metals Contained Within a Pb-Zn Waste Heap Exhibit Selective Association with Microbial Modules as Revealed by Network Analysis

Heavy metal contamination is a global environmental concern due to its persistence and toxicity. To explore soil microbial interaction mechanisms and their association with heavy metals on a Pb-Zn waste heap, ecological network analysis tools were used to analyze high-throughput data in microbiology. The microbial network was divided into several modules, but heavy metals were associated with specific modules. The heavy metal-tolerant module (M2) had a more negative than positive relationship with the heavy metal-mid-tolerant modules (M1 and M3). Tight coupling between fungal and bacterial operational taxonomic units (OTUs) within M2 was critical for module stability and heavy metal bioremediation. Additionally, members within M2 needed to form a positive relationship to cope with heavy metal contamination (As, Pb, Zn, Cu, and Cd). The study provides fundamental information for a deeper understanding of heavy metal bioremediation mechanisms in the Pb-Zn waste heap.

Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils

Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.

Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks

Soil contamination with multiple heavy metals poses threats to human health and ecosystem functioning. Using the Nemerow pollution index, which considers the effects of multiple heavy metals, we compared the diversity and composition of bacteria, fungi and protists and their potential interactions in response to a multi-metal contamination gradient. Multi-metal contamination significantly altered the community composition of bacteria, fungi and protists, and the degree of alteration increased with increasing severity of contamination. The alpha-diversity of bacteria, fungi and protists significantly decreased with increasing contamination level. The dominant generalists, found in all soil samples, were Gammaproteobacteria, Chloroflexi and Bacillus sp, whereas the dominant specialists were Anaerolineaceae, Entoloma sp. and Sandonidae_X sp. The relative abundances of generalists were positively correlated, whereas those of specialists were negatively correlated, with the Nemerow pollution index. In addition, the complexity of the microbial co-occurrence network increased with increasing contamination level. Generalists, rather than specialists, were the keystones in the microbial co-occurrence network and played a crucial role in adaptation to multi-metal contamination through enhanced potential interactions within the entire microbiome. Our results provide insights into the ecological effects of multi-metal contamination on the soil microbiome and will help to develop bio-remediation technologies for contaminated soils.

Improved degradation of petroleum hydrocarbons by co-culture of fungi and biosurfactant-producing bacteria

Microbial remediation has proven to be an effective technique for the cleanup of crude-oil contaminated sites. However, limited information exists on the dynamics involved in defined co-cultures of biosurfactant-producing bacteria and fungi in bioremediation processes. In this study, a fungal strain (Scedosporium sp. ZYY) capable of degrading petroleum hydrocarbons was isolated and co-cultured with biosurfactant-producing bacteria (Acinetobacter sp. Y2) to investigate their combined effect on crude-oil degradation. Results showed that the surface tension of the co-culture decreased from 63.12 to 47.58 mN m^-1, indicating the secretion of biosurfactants in the culture. Meanwhile, the degradation rate of total petroleum hydrocarbon increased from 23.36% to 58.61% at the end of the 7-d incubation period. In addition, gas chromatography - mass spectrometry analysis showed a significant (P < 0.05) degradation from 3789.27 mg/L to 940.33 mg/L for n-alkanes and 1667.33 μg/L to 661.5 μg/L for polycyclic aromatic hydrocarbons. Moreover, RT-qPCR results revealed the high expression of alkB and CYP52 genes by Acinetobacter sp. Y2 and Scedosporium sp. ZYY respectively in the co-culture, which corelated positively (P < 0.01) with n-alkane removal. Finally, microbial growth assay which corresponded with Fluorescein diacetate hydrolysis activity, highlighted the synergistic behavior of both strains in tackling the crude oil. Findings in this study suggest that the combination of fungal strain and biosurfactant-producing bacteria effectively enhances the degradation of petroleum hydrocarbons, which could shed new light on the improvement of bioremediation strategies.

Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea

Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.