Bacteria and fungi in soil

Written by Olaf Degen

Bacteria are the most abundant microorganisms in soil

Bacteria can be classified into various groups based on their function and metabolism including decomposers, nitrogen fixers, nitrifiers and denitrifiers. In addition, fungi are crucial for decomposing tough organic materials, such as cellulose and lignin. They form extensive networks of hyphae, which help in nutrient and water transport.

Soil in industrial and contaminated environments harbors various bacteria, some of which pose significant health risks to humans. Understanding the presence and pathogenic potential of these bacteria is crucial for public health, especially in mitigating the risks associated with industrial and environmental contamination. By monitoring and managing these bacterial populations, we can reduce their impact on human health and ensure safer environments.

Laboratory detection and identification of soil microbes involve several methods, ranging from traditional culture techniques (Plate counting, Light Microscopy) to advanced molecular approaches including MALDI-TOF Mass Spectrometry or DNA amplification and identification. MALDI-TOF Mass Spectrometry identifies microbes by analyzing the protein profiles of microbial cells starting from colony material and matching the fingerprint profiles to reference spectra. The laboratory can get identification results in minutes on species level with the MALDI Biotyper^® sirius.

With a database of more than 4,700 bacteria and fungi, Bruker covers a broad range of organisms in the reference library, and customers can add more strains in their site-specific reference library. Comparison of strains on species- and subspecies level at the same day, starting from colony material, is enabled by the IR Biotyper^®, based on FT-IR technology offering multiple options of strain discrimination.

Basic principle: Cell material of gram-positive, gram-negative bacteria, yeast or mould is applied to a MBT Biotarget 96 (96 sample positions), followed by adding a small droplet of "matrix" solution and air-drying. Once in the vacuum of the MALDI-TOF system, fast laser shots vaporize the sample's proteins, which are then separated according to their mass during their flight through the flight tube, towards the detector, resulting in a very specific proteomic fingerprint mass spectrum of the microorganism. This fingerprint is then matched against the Bruker reference library of fingerprints, covering more than 4700 species.

Below is a concise list of selected prominent soil bacteria found in industrial producers, battery producers, and rare soil environments, highlighting their species and pathogenicity.

Legionella pneumophila

Bacteria of the family Legionellaceae are responsible for Legionnaires' disease, a severe form of pneumonia caused by one main species Legionella pneumophila ⁽¹⁾. It spreads through inhalation of aerosolized water droplets containing the bacteria. Soil and water systems near industrial cooling towers and air conditioning units have been found to be contamination sources. Identification is possible with the MALDI Biotyper^® and discrimination of other species and serogroups 1 from 2-15 for Legionella pneumophila can be done with the IR Biotyper^® ^(2,3).

Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen known for causing infections in immunocompromised individuals. It can lead to respiratory infections, urinary tract infections, and septicemia. Its antibiotic resistance poses a significant challenge in treating this pathogen. Pseudomonas is present in industrial soils, especially those contaminated with heavy metals and chemicals, and identification of colonies is easy and accurate with the MALDI Biotyper^®.

Clostridia perfringens

Clostridium perfringens can cause gas gangrene and food poisoning. Its spores can survive in soil for extended periods, posing risks of contamination to food and wounds. Clostridia are present in agricultural and industrial soils, particularly where organic matter is abundant.

E. coli

Pathogenic strains of Escherichia coli, such as E. coli O157, can cause severe gastrointestinal illness, including diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS), which can be life-threatening. E. coli is often present in soil contaminated with human and animal waste, often found near industrial sites. Identification can be performed with the MALDI Biotyper^®, while discrimination of O- and H-groups is enabled by the IR Biotyper^®.

Reference Library

The Bruker MALDI Biotyper reference library is an ideal solution for identification of bacteria and fungi, including prominent species -listed above- or rare species described in environmental monitoring such as Virgibacillus, Lysinibacillus and other Bacilli, Kocuria, Acinetobacter and other species.

Rapid identification of soil microbes at the species level is crucial for timely decision-making in industry and environmental management. Advanced laboratory detection and identification methods like MALDI-TOF mass spectrometry and FT-IR have enhanced our ability to study these microorganisms, providing valuable insights into soil biodiversity and health. By leveraging rapid techniques and state-of-the art instruments like the MALDI Biotyper® sirius and IR Biotyper®, we can better understand and harness the power of soil microbes for a sustainable future.

Selected Literature

(1) Palusińska-Szysz and Cendrowska-Pinkosz. In Arch Immunol Ther Exp (Warsz) 2009. Pathogenicity of the family Legionellaceae. doi: 10.1007/s00005-009-0035-8

(2) Dilger et al. in J Microbiol Methods. 2016. Rapid and reliable identification of waterborne Legionella species by MALDI-TOF mass spectrometry. doi: 10.1016/j.mimet.2016.05.028.

(3) Pascale et al. in Front Microbiol. 2022. Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper System for Legionella pneumophila Serogroups Identification.
doi: 10.3389/fmicb.2022.866426.