Mikrobiological characterization 2017-2019
Microbiological characterization
Geochemical reactions that occur in actual acid sulfate soils have been elucidated and based on 16S rRNA gene studies, the microbial population structure is beginning to be understood. However, inferring microbial metabolic traits from 16S rRNA gene similarity is highly dubious and the genetic potential in populations responsible for the generation of actual acid sulfate soils is unknown. In addition, which microbes are active, and the metabolic pathways used between the oxidized zone (pH <4, an actual acid sulfate soil), transition zone (a steep pH gradient from acidic to near neutral), and the unoxidized sulfidic sediment (pH >7, potential acid sulfate soil) have so far been completely uninvestigated. We have aimed to take advantage of multi-omics and geochemical data to gain insights into the metabolic landscape and the molecular mechanisms underlying microbial life in this extreme environment.
In August 2017, soil was sampled from the oxidized acid sulfate soil, the transition zone and the original sulfidic sediment at the Risöfladan experimental field. DNA and RNA was isolated from all three soil zones in triplicates which were sent to the U.S. Department of Energy Joint Genome Institute (JGI) for metagenomic (DNA) and metatranscriptomics (RNA) sequencing. In addition to the sequencing data generated by JGI, a 16S rRNA gene sequencing, from the triplicate soil samples per zone, was performed. The sequencings were finished in November 2018 and publicly released in the beginning of 2019 at the NCBI Sequence Read Archive. A description of the sequencing data was published in 2019 in the journal Scientific Data in the article Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Geochemical analyses, pH and redox measurements, sulfur and iron speciation, and selected metal concentrations from the triplicate soil samples per zone were furthermore done at Åbo Akademi University in Turku and an overview of the geochemical data in the three soil zones can be seen in the picture below.
In order to investigate the biogeochemical relevance of the data, the assembled metagenomes were mapped to the metatranscriptomes by bioinformaticians at the Linnaeus University. The compiled sequence and geochemical data were published in 2022 in the journal Communications Earth & Environment in the article Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils.
The overall conclusions from the study were that the three soil zones showed very different key microbial communities and activities that could be linked to the geochemistry and that acid tolerant or moderately acidophilic iron oxidizing and sulfur metabolizing bacterial species dominated the transition zone during the catalysis of metal sulfide oxidation to form acid sulfate soil.
Key species and their dominating metabolic processes in the original sulfidic sediment can be seen in the picture below. In the original sulfide sediment anaerobic metabolic processes, e.g., methanogenesis, dominated. This soil zone also consisted of several poorly characterized populations.
