Bioprospecting of Extremophilic Microorganisms to Address Environmental Pollution

Summary

The isolation of heavy metal-resistant microbes from geothermal springs is a hot topic for the development of bioremediation and environmental monitoring biosystems. This study provides a methodological approach for isolating and identifying heavy metal tolerant bacteria from hot springs.

Abstract

Geothermal springs are rich in various metal ions due to the interaction between rock and water that takes place in the deep aquifer. Moreover, due to seasonality variation in pH and temperature, fluctuation in element composition is periodically observed within these extreme environments, influencing the environmental microbial communities. Extremophilic microorganisms that thrive in volcanic thermal vents have developed resistance mechanisms to handle several metal ions present in the environment, thus taking part to complex metal biogeochemical cycles. Moreover, extremophiles and their products have found an extensive foothold in the market, and this holds true especially for their enzymes. In this context, their characterization is functional to the development of biosystems and bioprocesses for environmental monitoring and bioremediation. To date, the isolation and cultivation under laboratory conditions of extremophilic microorganisms still represent a bottleneck for fully exploiting their biotechnological potential. This work describes a streamlined protocol for the isolation of thermophilic microorganisms from hot springs as well as their genotypical and phenotypical identification through the following steps: (1) Sampling of microorganisms from geothermal sites ("Pisciarelli", a volcanic area of Campi Flegrei in Naples, Italy); (2) Isolation of heavy metal resistant microorganisms; (3) Identification of microbial isolates; (4) Phenotypical characterization of the isolates. The methodologies described in this work might be generally applied also for the isolation of microorganisms from other extreme environments.

Introduction

The extreme environments on our planet are excellent sources of microorganisms capable of tolerating harsh conditions (i.e., temperature, pH, salinity, pressure, and heavy metals)^1,2, being Iceland, Italy, USA, New Zealand, Japan, Central Africa and India, the best-recognized and studied volcanic areas^{3,4,5,6,7,8,9}. Thermophiles have evolved in harsh environments in a range of temperatures from 45 °C to 80 °C^10,11,12. Thermophilic microorganisms, either belonging to the archaeal or bacterial kingdoms, are a reservoir for the study of biodiversity, phylogenesis, and the production of exclusive biomolecules for industrial applications ^13,14,15,16. Indeed, in the last decades, the continuous industrial demand in the global market has encouraged the exploitation of extremophiles and thermozymes for their diversified applications in several biotechnological fields ^17,18,19.

Hot springs, where organisms live in consortia, are rich sources of biodiversity, thus representing an attractive habitat to study microbial ecology^20,21. Moreover, these volcanic metal-rich areas are commonly colonized by microorganisms that have evolved tolerance systems to survive and adapt to the presence of heavy metals^22,23 and are therefore actively involved in their biogeochemical cycles. Nowadays, heavy metals are considered priority pollutants for humans and the environment. The heavy-metal-resistant microorganisms are able to solubilize and precipitate metals by transforming them and remodeling their ecosystems^24,25. The comprehension of the molecular mechanisms of heavy-metal resistance is a hot topic for the urgency to develop novel green approaches^26,27,28. In this context, the discovery of new tolerant bacteria represents the starting point for developing new strategies for environmental bioremediation^24,29. In accompanying the efforts to explore hydrothermal environments through microbiological procedures and increase knowledge on the role of the gene(s) underpinning heavy metal tolerance, a microbial screening was conducted in the hot-spring area of Campi Flegrei in Italy. This heavy metal-rich environment shows a powerful hydrothermal activity, fumarole, and boiling pools, variable in pH and temperature in dependence of seasonality, rainfall, and underground geological movements³⁰. In this perspective, we describe an easy-to-apply and efficacious way to isolate bacteria resistant to heavy metals, for example, Geobacillus stearothermophilus GF16³¹ (named as isolate 1) and Alicyclobacillus mali FL18³² (named as isolate 2) from Pisciarelli area of Campi Flegrei.

Protocol

1. Sampling of microorganisms from geothermal sites

1. Choose the site for sampling using as criterion places with desired temperature and pH. Measure the physical parameters through a digital thermocouple probe, inserting it into the selected pools or muds.
2. Collect 20 g of soils samples (in this case, from mud in the hydrothermal site of Pisciarelli Solfatara), picking them up with a sterilized spoon. Take at least two samples for each site chosen.
3. Put the samples in 50 mL sterile polypropylene tubes and immediately close.
4. Measure pH and temperature with a digital thermocouple probe by directly inserting it into the sampling site. After use, rinse the probe carefully with deionized water.

2. Isolation of heavy metal resistant microorganisms

NOTE: Perform steps 2.1-2.7 under a sterile biological hood.

1. Inoculate 2 g of each collected sample into 50 mL of freshly prepared Luria-Bertani medium (LB), in which the pH has been adjusted to 4 or 7 through the addition of HCl or NaOH.
2. Incubate the samples at the same temperature of the sampling site and at ±5 °C (55 °C and 60 °C for Pisciarelli samples) in a temperature-controlled orbital shaker for 24 h with a shaking rate of 180 rpm.
3. Plate 200 µL of the grown samples on LB agar (pH 4 or pH 7) and incubate in static condition for 48 h at 55 °C or 60 °C.
4. Isolate single colonies and repeat streak-plating cycles (steps 2.3 and 2.4) at least three times.
5. To prepare -80 °C frozen cell stocks, grow the cultures overnight (ON) and add to the grown cells 20% glycerol (in a final volume of 1 mL); use a mixture of acetone and dry ice for fast freezing.
6. To prepare an inoculum from a glycerol stock, inoculate 50 μL in 50 mL of LB (pH 4 or pH 6) and incubate at 55 °C or 60 °C in the orbital shaker at 180 rpm ON.
7. To obtain a growth profile, dilute a preculture (obtained from step 2.6) to 0.1 OD_{600 nm} in 10 mL of LB (pH 4 or pH 6), grow the cells at 55 °C or 60 °C for 16 h in the orbital shaker, and measure the OD_{600 nm} at 30 min intervals.
8. Construct a growth curve from the data obtained in step 2.7 with time (min) on X-axis and OD_{600 nm} on Y-axis.
9. Realize the same growth curve described in steps 2.7 and 2.8 but varying the pH (± 1 unit) of the culture medium (e.g., pH 3 and 5 for samples grown at pH 4) to determine the optimal pH for laboratory conditions.

3. Identification of microbial isolates

1. Preparation of genomic DNA
   1. Inoculate the isolate streaked from the glycerol stock in 50 mL of LB medium (pH 4 or pH 6) and grow in an orbital shaker at 55 °C or 60 °C at 180 rpm ON.
   2. Harvest the ON culture by centrifugation for 10 min at 5000 x g. Discard the supernatant.
   3. Prepare 10 mL of bacteria lysis buffer composed by: 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1.2% Triton X-100, and lysozyme (20 mg/mL) immediately before use.
   4. Resuspend the pellet in 180 µL of bacteria lysis buffer. Incubate for 30 min at 37 °C.
   5. Follow the guidelines indicated by a Genomic DNA Purification kit (Table of Materials) to extract genomic DNA.
   6. Quantify the extracted genomic DNA and its purity by UV-Vis measurement. For purity determine ratios-OD 260/280 nm and OD 260/230 nm.
   7. Assess the integrity of the genomic DNA by loading 200 ng of each sample on a 0.8% agarose gel and comparing the size distribution to a high-weight molecular marker.
   8. Commission to an external service the 16S rRNA fragment preparation, sequencing, and comparative analysis of the sequence obtained (1000 bp) with those present in the nucleotide database of the US National Center for Biotechnology Information (NCBI)³³.
2. To corroborate data of 16S rRNA sequencing, also perform automated ribotyping on the digested chromosomal DNA (external service, Table of Materials).
3. In the case in which the specie identification cannot be determined only with ribotyping data, commission a MALDI-TOF MS analysis for fatty acid identification.
4. To perform a phylogenetic analysis of the genus identified, analyze the 16S rRNA sequence of the isolate with BLASTn³⁴. Sequences with identities from 99% to 97% must be used to build a multiple sequence alignment using CLUSTAL Omega³⁵. Construct a neighbor-joining tree using the default option of ClustalW2 (Simple Phylogeny).

4. Heavy-metals and antibiotics susceptibility

1. Inoculate the isolate from a glycerol stock (see step 2.5) and grow it in 200 mL of LB under the optimal pH and temperature conditions previously determined.
2. Dilute each preculture at 0.1 OD_{600 nm} in 5 mL of LB medium (at the appropriate pH) containing increasing concentrations of heavy metals. The concentrations vary from 0.01-120 mM for heavy metals [As(V), As(III), Cd(II), Co(III), Cr(VI), Cu(II), Hg(II), Ni(II), V(V)] or 0.5-1 mg/mL for the antibiotics [Ampicillin, Bacitracin, Chloramphenicol, Ciprofloxacin, Erythromycin, Kanamycin, Streptomycin, Tetracycline, and Vancomycin].
3. Perform heavy metal and antibiotic treatments separately. Use a 50 mL polypropylene tube and grow the cells in a temperature-controlled orbital shaker with a shaking rate of 180 rpm at 55 °C or 60°C for 16 h for each condition/treatment.
4. Calculate Minimum Inhibitory Concentration (MIC) either for antibiotics or heavy metals by identifying the concentration values in the tubes where microbial growth does not occur, i.e., determining the values that completely inhibit cell growth after 16 h.
5. Check that the concentration is inhibitory and not lethal for the cells by plating 200 μL of the culture grown at the value that is considered as MIC on LB-agar plates (at the appropriate pH and temperature) and verifying the presence of colonies after ON incubation.
   NOTE: Since the culture on LB agar plate is viable at 4 °C only for a few weeks, in order to preserve the isolates for a longer time, glycerol stocks were prepared and stored at -80 °C. For MIC determination, at least three independent replicates using independent cultures were carried out. The standard deviation was calculated among triplicate experiments.

Results

Sampling site
This protocol illustrates a method for the isolation of heavy metal-resistant bacteria from a hot spring. In this study, the Pisciarelli area, an acid-sulfidic geothermal environment, was used as a sampling site (Figure 1). This ecosystem is characterized by the flow of aggressive sulfurous fluids derived from volcanic activities. It has been demonstrated that the microbial communities in acid-sulfidic geothermal systems are subjected to ex...

Discussion

Hot springs contain an untapped diversity of microbiomes with equally diverse metabolic capacities¹². The development of strategies for the isolation of microorganisms that can efficiently convert heavy metals into less toxic compounds¹⁰ represents a research area of growing interest worldwide. This paper aims to describe a streamlined approach for the screening and isolation of microbes with the ability to resist toxic chemicals. The method described can be easily modified...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Ampicillin	Sigma Aldrich	A9393
Aura Mini	bio air s.c.r.l.		Biological hood
Bacitracin	Sigma Aldrich	B0125
Cadmium chloride	Sigma Aldrich	202908
Chloramphenicol	Sigma Aldrich	C0378
Ciprofloxacin	Sigma Aldrich	17850
Cobalt chloride	Sigma Aldrich	C8661
Copper chloride	Sigma Aldrich	224332
Erythromycin	Sigma Aldrich	E5389
Exernal Service	DSMZ		Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
Genomic DNA Purification Kit	Thermo Scientific	#K0721
Kanamycin sulphate	Sigma Aldrich	60615
MaxQTM 4000 Benchtop Orbital Shaker	Thermo Scientific	SHKE4000
Mercury chloride	Sigma Aldrich	215465
NanoDrop 1000 Spectrophotometer	Thermo Scientific
Nickel chloride	Sigma Aldrich	654507
Orion Star A221 Portable pH Meter	Thermo Scientific	STARA2218
Sodium (meta) arsenite	Sigma Aldrich	S7400
Sodium arsenate dibasic heptahydrate	Sigma Aldrich	A6756
Sodium chloride	Sigma Aldrich	S5886
Streptomycin	Sigma Aldrich	S6501
Tetracycline	Sigma Aldrich	87128
Tryptone BioChemica	Applichem Panreac	A1553
Vancomycin	Sigma Aldrich	PHR1732
Yeast extract for molecular biology	Applichem Panreac	A3732