Introduction

Heavy metals (HMs) pose a serious threat to mankind through increased levels in agricultural lands, water bodies, and natural ecosystems. They can be categorized into non-essential metals (As, Cd, Cr, Hg, Ni, and Pb) and essential metals (Cu, Fe, and Zn) (Carrillo-González and González-Chávez 2012). Various sources of HMs include agricultural activity, industrial effluents, fertilizers, mining, and solid waste dumping sites as well as atmospheric sources. Toxic metals have no role in biological pathways and their excess can induce dermatitis, cancer, damage to renal circulation, liver, and nervous tissues, while long-term exposure may lead to death (Jaishankar et al. 2014). As industrialization train is unstoppable, fight with heavy metal contamination needs innovative remediation strategies. Awareness for treatment and remediation of metal-containing wastes to threshold level before release into natural environment has been growing globally.

Efficient, cost-effective, and environment-friendly practices are needed for fine-tuning of waste management. Microbial application is considered an economic and efficient way to remediate HMs from water and soil (Ahirwar et al. 2016). Microbes can use inorganic contaminants as a source of energy via activating metabolic processes. Success of the bioremediation process depends upon the nature, degree and depth of contaminants, polluted site, environmental policies, and cost. Besides, other factors like pH, temperature, nutrient level, oxygen concentrations, and abiotic factors also affect bioremediation. The high surface-to-volume ratio of microbes and their potential to remediate metals are considered as the key reason to prefer them.

Studies have demonstrated that indigenous strains that reside in the polluted environments have a significant ability to endure toxic metals. Among the microbial entities, filamentous fungi can grow rapidly and survive in harsh environments. On the contrary, bacteria are ubiquitous biological entities on earth that can reproduce and survive in a variety of environments due to their small size, ease of cultivation on a variety of media, and rapid growth (Yin et al. 2019). Over time, they have developed resistance against toxic metals to survive in polluted areas because of the high surface-to-volume ratio.

Mostly, metal-resistant fungal strains have been suggested as bioagents for remediating metal-contaminated sites (Chang et al. 2019). The composition of fungal cell wall provides active sites for metal sequestration. Preliminary step in the biosorption is a passive process involving various metal-binding activities like physical adsorption, ion exchange, and complexations, while active process allows the metal to penetrate in the cells. Bacterial application for remediation is a low-input biotechnological practice that is safer and more reliable than conventional methods, and can improve soil fertility, characteristics, and quality. For remediation of polluted sites, different resistant bacterial strains have been used for decades (Krishnamoorthy et al. 2017). The mechanisms adopted by bacteria to detoxify the metal contaminants are metal exclusion, active transport of metal, biosorption, bioaccumulation, biomineralization, and biotransformation.

Metal-resistant plant growth-promoting microbes are being used to control the metalliferous sites in a productive and eco-friendly way (Dotaniya et al. 2018). These microbes not only boost the plant growth process by producing chelators but also reduce the availability of metals to plants. The aim to remediate metals is possible only if the biological entities can resist and tolerate the toxic metals by their physiological and molecular mechanisms (Yan et al. 2020). Trichoderma pseudokoningii, isolated from TSW, along with AM fungi has been shown to improve growth of Tagetes patula in TSW amended soil (Bareen and Nazir 2010). Moreover, a synergistic interaction has been observed among Trichoderma pseudokoningii and natural or synthetic PGRs to improve growth in pearl millet grown in TSW amended soil (Bareen et al. 2012).

Tannery solid waste represents a metal toxic environmental situation, and it is presumed that it can harbor metal-resistant microbes. This is the first comprehensive study of autochthonous microbes from tannery solid waste and their tolerance levels and biosorption efficiency against HMs. The objective was to isolate and characterize the heavy metal resistance of strains of fungi and bacteria against a particular metal or multi-metal environment and to observe the most efficient multi-metal-resistant strains in synthetic metal solutions. The final step was to identify the potent strains on a molecular basis for possible future use in bioremediation of metal laden environment.

Materials and methods

Sampling of tannery solid waste

Tannery solid-waste samples were gathered from solid-waste landfill site of KTWMA, Depalpur Road, Kasur, Pakistan. Twenty-five random samples were collected with at least 10 m distance between every two samples. The material was taken in pre-labeled sterile bags, transported to the laboratory, and stored at 4 °C for further use.

Isolation of fungi

One gram of TSW sample from each bag was suspended into 10 mL of sterile water followed by serial dilutions up to 106. About 50 µL dilution was pipetted on 2% ME agar plates using a glass spreader under complete aseptic conditions in a culture room followed by incubation at 25 ± 3 °C for 5–7 days. The fungal colonies that appeared were isolated in new plates. Fungal strains were purified as single spore isolates from mature cultures by spreading conidia with a sterile platinum loop.

Morphological characterization of fungal strains

The fungal strains grown on ME agar medium were morphologically characterized. For slide preparation, a small mycelial plug was mounted onto the slide in lactophenol followed by observation under compound microscope. The morphological characterization up to genus level was performed according to the taxonomic key provided by Samson et al. (2014) and Pitt and Hocking (2009).

Isolation of bacteria

One gram of TSW sample was mixed into 10 mL of autoclaved distilled water and serial dilutions (up to 106) were prepared. Using spread plate method, 50 µL sample was pipetted onto LB agar plates followed by incubation at 37 °C for 24 h. Based on morphological properties, bacterial colonies were selected and streaked on new agar plates to get single purified colonies.

Biochemical characterization of bacterial strains

The biochemical characterization of bacterial strains was performed by the methods of Cappuccino and Sherman (2014). The test performed under biochemical characterization were gram staining, spore staining, catalase, oxidase, starch test, Voges Proskauer, and methyl red.

Heavy metal resistance assay of fungi

Metal resistance ability of isolated fungal strains was determined by following the protocol of Acosta-Rodríguez et al. (2018). Pour plate method was selected for screening the resistant fungal strains against Cd, Cr, Cu, Hg, Pb, and Zn. The ME agar medium was modified with different metal concentrations ranging from 10 to 1050 mg L−1. Fungal disc of 3 mm size with actively growing hyphae was cut aseptically from each isolate and cultured on ME agar plate followed by incubation at 25 ± 3 °C for 7 days. After incubation, the growth of fungal strains on metal-containing and control plates was observed. The strains showing resistance at low metal concentration were exposed to higher concentrations and minimum inhibitory concentration (MIC) of each strain against the metal was determined.

Heavy metal resistance assay of bacteria

Metal resistance potential of isolated strains was determined by following the method of Hassen et al. (1998). Agar well-diffusion technique was used for screening of metal-resistant bacterial strains against Cd, Cr, Cu, Hg, Pb, and Zn. After incubation at 37 °C for 24 h, the zone of inhibition was measured as an indicator of sensitivity. The strains showing resistance at low concentrations were further exposed to high concentrations and their sensitivity was measured.

Metal biosorption potential of fungal strains

Based on the metal resistance assay, five fungal strains having the maximum metal resistance potential were chosen for biosorption test. Biosorption efficiency of the selected resistant strains was observed at 500 mg L−1 concentration (Pb, Cr, and Zn) and 200 mg L−1 (Cd and Cu). A 5 mm disc from edge of colony of the respective fungus on ME agar medium having actively growing mycelium was cut aseptically and suspended into metal-containing ME broth medium. Flasks were incubated at 25 ± 3 °C on an orbital shaker set at 150 rpm for 7–10 days followed by filtration. The supernatant was digested in nitric acid and perchloric acid (3:1 ratio), followed by filtration (Whatman no. 42). The sample was diluted up to 50 mL with distilled water (Javaid et al. 2010). The total metal concentration was determined on an atomic absorption spectrophotometer and the biosorption efficiency (%) was calculated by the formula

$$\mathrm{Biosorption efficiency }(\mathrm{\%}) = \frac{{C}_{\mathrm{i}}-{C}_{\mathrm{e}}}{{C}_{\mathrm{e}}} \times 100,$$

where Ci represents initial concentration of metal in the solution and Ce represents final concentration of metal in the solution at equilibrium.

Metal biosorption potential of resistant bacterial strains

The ten strains having maximum metal resistance were selected and inoculated into LB broth medium followed by incubation at 37 °C and 150 rpm until the O.D reached 0.6 at 600 nm. Metal solution (Cd, Cr, Cu, Hg, Pb, and Zn) of 500 mg L−1 concentration was added into each flask separately including control. Flasks were re-incubated at 37 °C for 24 h followed by centrifugation at 5000 rpm for 15–20 min. The supernatant was collected and digested in double volume of concentrated nitric acid on a hot plate at 100 °C until the volume reduced to half. The sample was filtered through filter paper (Whatman no. 42) and diluted up to 100 mL using distilled water. The reduction in total metal content was determined on an atomic absorption spectrophotometer and the metal biosorption capacity (%) was calculated following the method of Marzan et al. (2017).

Molecular characterization of resistant fungal strains

DNA extraction

DNA of the five resistant Trichoderma strains was extracted using CTAB method (Aamir et al. 2015). Lyophilized fungal mycelia were homogenized in 2% CTAB extraction buffer followed by incubation at 65 °C. After centrifugation, the supernatant was collected in a new microcentrifuge tube and 2 µL of RNase was added into the reaction mixture succeeded by incubation at 37 °C for 15 min. Next, purification step was carried out by adding an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) followed by centrifugation at 13,000 rpm for 10 min. An equal volume of ice-cold isopropanol was mixed with the upper collected aqueous layer followed by incubation at − 20 °C for 30 min. After centrifugation, DNA pellet was washed with 500 µL of 70% ethanol followed by centrifugation at 12,000 rpm for 5 min. Ethanol was discarded, and DNA pellet was dried and dissolved in 50 µL of TE buffer for further use.

PCR amplification

To carry out PCR reaction, 50 μL reaction mixture was prepared by adding 2 μL of template DNA (30–35 ng), 10 μL of 5 × Phusion buffer, 1 μL of 10 mM dNTPs, 0.5 μL Taq polymerase, and 2.5 μL of 10 mM primer solutions i.e., forward ITS1F (5′-TCCGTAGGTGAACCTGCGG-3′) and reverse ITS4R (5′-TCCTCCGCTTATTGATATGC-3′) primers were used to amplify the ITS1 and ITS2 region. The PCR conditions were set with an initial denaturation at 98 °C for 1 min followed by annealing at 50.8 °C for 1 min and extension at 72 °C for 1 min. Final extension was performed at 72 °C for 10 min. The PCR products were visualized in 1% agarose gel (w/v) having 0.1 μg mL−1 SYBR safe and visualized in gel-doc imaging software.

DNA sequencing

The PCR products were submitted to the Cornell Institute of Biotechnology for di-deoxy Sanger DNA sequencing and the obtained sequences were subjected to nucleotide BLAST database via NCBI website (http://www.ncbi.nlm.nih.gov) to determine their homology. The sequences were submitted to NCBI GenBank and accession numbers were obtained. For sequence identification variation, all sequences were clustered using Clustal Omega software (http://www.ebi.ac.uk/).

Molecular characterization of resistant bacterial strains

DNA extraction

DNA of ten resistant Bacillus strains was extracted using Thermo Scientific GeneJet genomic DNA purification kit.

PCR amplification

To perform PCR, 25 μL reaction mixture was prepared by adding 1 μL of template DNA (25–35 ng), 12.50 μL of Phusion PCR master mix and 1.25 μL of 10 μM primer solutions, i.e., forward (5′-AGA GTT TGA TCC TGG CTC AG-3′) and reverse primer (5′-GGT TAC CTT GTT ACG ACT T-3′), were used to amplify the 16s rRNA region. The PCR conditions were set with an initial denaturation at 98 °C for 30 s followed by 30 cycles (denaturation at 98 °C for 10 s, annealing at 56 °C for 30 s, and extension at 72 °C for 30 s). The final extension was performed at 72 °C for 5 min. PCR products were run in 1% (w/v) agarose gel with 0.1 μg mL−1 SYBR safe followed by bands’ visualization using gel-doc Imaging software.

DNA sequencing

The PCR products were submitted to the Cornell Institute of Biotechnology for di-deoxy Sanger DNA sequencing. Percent homology of sequenced strains was checked using the nucleotide blast database through NCBI. The sequences were submitted to NCBI GenBank and accession numbers were obtained. For sequence identification variation, all sequences were clustered using Clustal Omega software (http://www.ebi.ac.uk/).

Results and discussion

Morphological characterization of fungal strains

A total of 12 strains of fungi were isolated from TSW and were characterized up to genus level and some to the species level, based on colony morphology and microscopic characteristics (Table 1, Fig. 1). Among the isolates, one strain belonged to Alternaria, three to Aspergillus, two to Fusarium, and six to Trichoderma (Table 2). Trichoderma species have been widely reported from tannery effluent (Sharma and Malaviya 2018), tannery solid waste (Bareen and Nazir, 2010), municipal solid waste (Gautam et al. 2012), metal-contaminated soil (Kacprzak et al. 2014), and mining sites (Oladipo et al. 2018). Numerous studies have shown that Trichoderma species resist a high concentration of metals and also improve plant growth under metal stressed environment (Zhang et al. 2020). The genera of fungi isolated from TSW in the present study have already been observed at metal-contaminated sites.

Table 1 Colony characteristics of the isolated filamentous fungi
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Fig. 1
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Colony morphology and microphotographs of filamentous fungi isolated from TSW on ME agar medium

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Table 2 The number of fungal strains in each genus isolated from TSW
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Biochemical characterization of bacterial strains

A total of 25 bacterial colonies were isolated from TSW. Morphological observations revealed that most of the strains to be rod shaped, while only five were round (Table 3). Strains TSW-3, TSW-4, TSW-7, TSW-19, and TSW-24 were Gram-negative and all others were Gram-positive. Except for TSW-6, TSW-7, TSW-10, TSW-18, TSW-20, and TSW-22, all remaining strains were catalase positive. Most of the strains showed positive results for the oxidase test except TSW-3, TSW-4, TSW-7, TSW-13, TSW-19, and TSW-24. Out of 25 bacterial strains, ten strains demonstrated positive results for MR test, while seven strains were found positive for the VP test. Based on the biochemical characteristics, the isolates were identified up to the genus level as Micrococcus spp., Bacillus spp., Klebsiella spp., Escherichia sp., Pseudomonas spp., and Streptococcus spp. (Table 4). Similar results were demonstrated by Khan et al. (2019), who isolated Pseudomonas spp., Bacillus spp., and Alcaligens spp. from leather dye.

Table 3 Biochemical characteristics of isolated bacterial strains
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Table 4 The number of bacterial strains isolated from TSW
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Heavy metal resistance assay of fungal strains

Tanning industries are considered the major source of metal contaminants; therefore, isolation of metal-resistant fungal strains from such sites may play a vital role in the bioremediation of contaminated sites. In the current study, 12 strains of filamentous fungi were isolated from the tannery solid waste. The maximum metal resistance potential of each was studied against six different metals by culturing them on metal-containing ME agar plates. The MICs of the isolated strains for each metal were determined as shown in the form of a heatmap in Table 5. The resistance of isolated fungi to the studied metals was in the order of Pb > Cr > Zn > Cu > Cd > Hg. The behavior of metal-resistant strains for more than one metal is also shown in Fig. 2.

Table 5 Minimum inhibitory concentration (MIC) of fungal strains isolated from TSW against six different metals (mg L−1) shown in the form of a heatmap
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Fig. 2
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Venn diagram showing the behavior of metal-resistant filamentous fungal strains for Cd, Cr, Cu, Hg, Pb, and Zn. Among isolated strains (n = 12), 4 Cd resistant (300–400 mg L−1), 6 Cr resistant (700–800 mg L−1), 6 Cu resistant (350–450 mg L−1), 7 Hg resistant (50–100 mg L−1), 3 Pb resistant (950–1050 mg L−1), and 5 Zn resistant (550–650 mg L−1) strains were arranged using Venn diagram

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In our study, Trichoderma and Aspergillus niger showed maximum resistance against the different metals. Several filamentous fungal genera like Aspergillus, Fusarium, Trichoderma, Humicola, and Nannizzia have been reported as metal-resistant genera (Iram et al. 2013). Increase in metal concentration caused a decrease in fungal growth. The decrease in fungal biomass may appear to be due to high metal concentration and particular MIC of isolated strains. Iram et al. (2013) reported that fungal resistance to toxic metals may be attributed to the presence of an effective resistance mechanism. The maximum resistance was observed against Cr and Pb over others. Various resistance mechanisms adopted by fungi for remediation of contaminants include adsorption, oxidation, reduction, methylation, and detoxification. Analogous to our findings, Oladipo et al. (2018) reported that Trichoderma, Rhizopus, and Fomitopsis isolated from gold mining sites could resist 400–1000 mg kg−1 Pb, Cu, Fe and 25 mg kg−1 Cd. Mohammadian et al. (2017) reported that Trichoderma spp. have the maximum tolerance level against Cd, Cr, Cu, Ni, Pb, and Zn. Our study has shown that fungi isolated from TSW have a good resistance against all heavy metals.

Heavy metal resistance assay for bacterial strains

A good resistance against different metals was observed in all bacterial strains by zone inhibition plate assay. Diversified results were observed for isolated bacterial strains as shown in the heatmap (Table 6) along with the order of heavy metal resistance against six different metals. The behavior of metal-resistant strains for more than one metal is depicted in Fig. 3. The bacterial growth at high metal concentrations appears to be due to the presence of an effective resistance mechanism for metal detoxification, such as metal efflux, intracellular sequestration, binding with bacterial cell envelopes, and metal reduction. Some of the important bacterial genera used in the remediation of metal-contaminated sites are Bacillus, Pseudomonas, Acinetobacter, and Enterococcus (Nath et al. 2019). High metal concentration may lead to a decrease in the growth and biochemical activities of strains, whereas resistant strains have the potential to reproduce at high concentrations.

Table 6 Minimum inhibitory concentration (MIC) of bacterial isolates against six different metals (mg L−1)
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Fig. 3
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Venn diagram showing the behavior of metal-resistant bacterial strains for Cd, Cr, Cu, Hg, Pb, and Zn. Among isolated strains (n = 25), 2 Cd resistant (600 mg L−1), 4 Cr resistant (950 mg L−1), 5 Cu resistant (650 mg L−1), 6 Hg resistant (50 mg L−1), 3 Pb resistant (1200–1050 mg L−1), and 3 Zn resistant (700 mg L−1) strains were arranged using Venn diagram

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Metal biosorption potential of fungal strains

Biosorption potential of five HM-resistant strains against synthetic metal solutions is shown in Fig. 4. The strain TSW-10 exhibited 73.7% for Cr, and TSW-11 exhibited 71.8% for Cu, whereas TSW-3 showed biosorption potential of 81.7% for Pb. Fungi have a better biosorption potential because of the nature of their cell wall and the functional groups involved in metal binding. According to Kapahi and Sachdeva (2019), among various functional groups, amine and carboxylate groups are important binding sites for metal attachment and biosorption in fungi. In the current study, metal-resistant strains selected for biosorption showed the maximum removal efficiency for Pb, Cr, and Zn compared to Cu and Cd. Comparable results have been shown by Kumar and Dwivedi (2019) that a high level of Cr could be remediated by applying Trichoderma spp. However, the success of metal biosorption by fungi depends on the type and concentration of metal, physiological, and environmental conditions, availability of nutrients, and fungal species (Kapahi and Sachdeva 2019). Researchers have reported that fungal strains such as Aspergillus niger, A. terreus, Trichoderma harzianum, and Rhizopus oryzae survive in high metal concentrations (Mishra and Malik 2014). Similarly, Liaquat et al. (2020) have shown that Rhizopus and Trichoderma spp. could resist high concentration of Pb, Cr, and Cd. In fact, the presence of Trichoderma in highly toxic metal laden environments, already documented by many researchers, has been confirmed in the present study. The fungal strains TSW-3, TSW-10, and TSW-11 showed multi-metal resistance and biosorption and can therefore be employed to clean media contaminated with metals, may be water or soil.

Fig. 4
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Biosorption efficiency (%) of selected resistant fungal strains against their respective potential metal concentrations, at 200 mg L−1 (Cd and Cu) and 500 mg L−1 (Cr, Pb, and Zn)

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Metal biosorption potential of bacterial strains

Among the 25 strains, TSW-06 and TSW-17 showed maximum biosorption potential for Pb, i.e., 86.8 and 80.7%, whereas, for Cr, 79.2, 89.8, and 74.3% biosorption potential was exhibited by TSW-02, TSW-14, and TSW-15, respectively. For Zn, 87.5 and 80.7% biosorption potential was revealed by TSW-19 and TSW-22 (Fig. 5). Among all strains, the maximum biosorption for Pb was observed by the two fungal strains. The reason for high Pb sorption may be attributed to high atomic weight compared to others, which makes it to interact readily with biological components. Three fungal strains showed good biosorption for Cr. Thatheyus and Ramya (2016) stated that chromium-resistant strains have the potential to biosorb Cr in the living system either by binding it on the cell wall surface or precipitating it with anions or polymers secreted by bacteria. In the current study, the reason for better biosorption potential of Cr and Zn could be due to the availability of anionic functional groups on bacterial surfaces. The Gram-negative strains exhibited better resistance and biosorption for Pb and Zn compared to Cr, Cu, and Cd. It is worthwhile to mention that none of the bacterial strains showed multi-metal biosorption, rather individual strains showed affinity for particular metals.

Fig. 5
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Biosorption capacity (%) of selected resistant bacterial strains at 500 mg L−1 concentration of their respective potential metal

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Molecular characterization of fungal strains

Kingdom fungi is considered the second largest eukaryotic group, ranging from 1.5 to 5.1 million species on earth. Mycologists have encountered the problem of identifying and classifying the wide genera of fungi from a taxonomic perspective. For species-level identification, the ITS regions are considered the fastest and useful part of the rRNA cistron. Over 3 decades ago, fungal nuclear ribosomal operon primers were used for molecular identification of fungi (White et al. 1990) which helped to generate the sequence of smaller subunit, i.e., nrSSU-18S, larger subunit i.e., nrLSU-26S or 28S, and Internal Transcribed Spacer (ITS) region i.e., ITS1, 5.8S, ITS2. Schoch et al. (2012) reported that the maximum likelihood of correct fungal identification could be achieved by sequencing ITS regions. Compared to conventional methods, PCR and Sanger sequencing have been overwhelmingly used for fungal ITS, i.e., ITS1, ITS2 and 5.8S. Five metal-resistant Trichoderma strains were molecularly characterized by amplifying and sequencing ITS1 and ITS2 regions as given by Oskiera et al. (2015). The sequence analysis of ITS region revealed that all the five strains belonged to the genus Trichoderma. The accession numbers allocated by NCBI for sequenced Trichoderma strains are given in Table 7. The statistical analysis of the phylogenetic tree (MEGA Version 10.1.8), generated by bootstrapping (100) and maximum likelihood method showed the similarity index of all the studied sequenced strains with NCBI reported known species as displayed in Fig. 6. The isolated Trichoderma spp. were characterized as Trichoderma lixii (MW042868.1), Trichoderma pseudokoningii (MW042872.1), Trichoderma pseudokoningii (MW042876.1), Trichoderma hamatum (MW042877.1), and Trichoderma harzianum (MW042899.1).

Table 7 The accession numbers and BLAST results of selected fungal strains from the NCBI ITS region database
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Fig. 6
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Phylogenetic relationship of five metal-resistant strains of Trichoderma isolated from TSW

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Multiple sequence alignments of sequenced fungal strains

Clustal W analysis of DNA sequences of five fungi belonging to the genus Trichoderma was executed using bioinformatics tool, i.e., Clustal Omega software. The results showed presence of more variation compared to conserved regions, as shown in Fig. 7. It was observed that out of the total aligned sequences, 173 bp-long conserved region was observed among DNA sequences of characterized Trichoderma strains, symbolized by asterisk. The strains which had more matched base pairs were considered close to each other and vice versa. In the current study, TSWF-3 and TSWF-10 had more matched and less mismatched base pairs and both were identified as T. pseudokoningii. Among all strains, more genetic variation was noted in Trichoderma harzianum followed by Trichoderma hamatum and the variation was represented by ‘grey highlighted area’ in the sequence (Fig. 7). Nevo (2011) stated that environmental stress may lead to a high molecular diversity and genetic variability. In the current study, the possible reason for genetic variation seems to be metal stress in the environment.

Fig. 7
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Multiple sequence alignment of different metal-resistant Trichoderma strains showing conserved sequences with “asterisk symbol”, and genetic variations with “grey highlights”

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Molecular characterization of selected bacterial strains

The ten strains of bacteria exhibiting best metal resistance were molecularly identified using 16S rRNA ribotyping technique. The accession numbers of the selected bacterial strains allocated by NCBI are given in Table 8. Constructed dendrogram results distinguished those selected strains to belong to Bacillus. Statistical analysis of the constructed phylogenetic tree (MEGA Version 10.1.8), generated by the maximum likelihood method and bootstrapping (100), showed the similarity index of all the selected strains (Fig. 8). The Bacillus species isolated in this study were identified as Bacillus xiamenensis (MT809704.1), B. velezensis (MT809705.1), B. piscis (MT809706.1), B. safensis (MT809709.1), B. subtilis (MT810012.1), B. subtilis (MT809752.1), B. subtilis (MT819963.1), B. licheniformis (MT812984.1), B. cereus (MT814215.1), and B. thuringiensis (MT814283.1). This is the first report of isolation of different Bacillus strains from tannery solid waste.

Table 8 The accession numbers by NCBI of the selected bacterial strains by 16S rRNA ribotyping
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Fig. 8
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Phylogenetic tree constructed using MEGA software. Maximum-likelihood tree showing the evolutionary relationship between sorted metal-resistant bacterial strains (TSW-2, TSW-5, TSW-6, TSW-10, TSW-14, TSW-15, TSW-17, TSW-19, TSW-20, and TSW-22) and previously reported strains having the highest % homology from NCBI GenBank

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Multiple sequence alignments of sequenced bacterial strains

Clustal W analysis of DNA sequences of ten different metal-resistant bacterial strains belonging to the genus Bacillus was performed using bioinformatics tool, i.e., Clustal Omega software. The results illustrated major ratio of varied region compared to conserved regions as exhibited in Fig. 9. Among the aligned sequences, 90 bp-long conserved region was observed among DNA sequences of characterized Bacillus strains, symbolized by asterisk. The strains which had more matched base pairs were deemed close to each other and vice versa. Our finding showed that TSW-14, TSW-15, and TSW-22 had more matched and less mismatched base pairs and all three were named Bacillus subtilis. Among all strains, more genetic variation was observed in B. thuringiensis accompanied by B. licheniformis and the sequence with variation was denoted by ‘grey highlighted area’ in the sequence (Fig. 9). The possible reasons for these genetic variations may be attributed to attainability of metal stress environments to microbes.

Fig. 9
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Multiple sequence alignment of different metal-resistant Bacillus strains showing conserved sequences with asterisks, and genetic variations with grey highlights

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Conclusion

Autochthonous microbes isolated from HM polluted environment have the potential to grow and survive in such environment. A variety of filamentous fungi and bacteria isolated from TSW indicated five species of Trichoderma and ten of Bacillus with a good tolerance and biosorption potential for metals. Molecular characterization indicated the fungi to be T. hamatum, T. harzianum, T. lixii, and two strains of T. psuedokoningii. On the other hand, the ten bacterial strains were found to be B. xiamenensis, B. velezensis, B. piscis, B. safensis, B. licheniformis, B. cereus, B. thuringiensis, and three strains of B. subtilis. The fungal strains T. pseudokoningii (TSW-3, TSW-10) and T. harzianum showed a multi-metal tolerance and resistance. Bacteria exhibited metal-specific tolerance and resistance, Bacillus xiamenensis, B. subtilis (TSW-14) and B. subtilis (TSW-15) against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. Thus, the efficient microbial flora can be employed in removing metals from contaminated soil and water.