Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.

Iron‑sulfur geochemistry and acidity retention in hydrologically active macropores of boreal acid sulfate soils: Effects of mitigation suspensions of fine-grained calcite and peat

Acid sulfate soils discharge large amounts of sulfuric acid along with toxic metals, deteriorating water quality and ecosystem health of recipient waterbodies. There is thus an urgent need to develop cost-effective and sustainable measures to mitigate the negative effects of these soils. In this study, we flushed aseptically-prepared MQ water (reference) or mitigation suspensions containing calcite, peat or a combination of both through 15-cm-thick soil cores from an acid sulfate soil field in western Finland, and investigated the geochemistry of Fe and S on the surfaces of macropores and in the solid columnar blocks (interiors) of the soil columns. The macropore surfaces of all soil columns were strongly enriched in total and HCl-extractable Fe and S relative to the interiors, owing to the existence of abundant Fe oxyhydroxysulfates (schwertmannite and partly jarosite) as yellow-to-brownish surface-coatings. The dissolution/hydrolysis of Fe oxyhydroxysulfates (predominantly jarosite) on the macropore surfaces of the reference columns, although being constantly flushed, effectively buffered the permeates at pH close to 4. These results suggest that Fe oxyhydroxysulfates accumulated on the macropore surfaces of boreal acid sulfate soils can act as long-lasting acidification sources. The treatments with mitigation suspensions led to a (near-)complete conversion of jarosite to Fe hydroxides, causing a substantial loss of S. In contrast, we did not observe any recognizable evidence indicating transformation of schwertmannite. However, sulfate sorbed by this mineral might be partially lost through anion-exchange processes during the treatments with calcite. No Fe sulfides were found in the peat-treated columns. Since Fe sulfides can support renewed acidification events, the moderate mineralogical changes induced by peat are desirable. In addition, peat materials can act as toxic-metal scavengers. Thus, the peat materials used here, which is relatively cheap in the boreal zone, is ideal for remediating boreal acid sulfate soils and other similar jarosite-bearing soils.

Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials

Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil. The pH of the dredge spoils decreased with time indicating metal sulfide oxidation and resulted in elevated sulfate concentrations along with a concomitant release of metals. However, calculations indicated only approximately 5% of the added lime had been dissolved. The bacterial communities decreased in diversity with the lowering of the pH as taxa most similar to extremely acidophilic sulfur, and in some cases iron, oxidizing Acidithiobacillus species became the dominant characterized genus in the deposited dredge spoils as the oxidation front moved deeper. In addition, other taxa characterized as involved in oxidation of iron or sulfur were identified including Gallionella, Sulfuricurvum, and Sulfurimonas. These data suggest there was a rapid conversion of the dredge spoils to severely acidic soil similar to actual acid sulfate soil and that the lime placed on the land prior to deposition of the spoils, and later ploughed into the dry dredge spoils, was insufficient to halt this process. Hence, future dredging and deposition of dredge spoils containing metal sulfides should not only take into account the amount of lime used for buffering but also its grain size and mixing into the soil.

Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments

Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidized layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.

Indirect DNA extraction method suitable for acidic soil with high clay content

DNA extraction is an essential procedure when investigating microbial communities in environmental samples by sequencing technologies. High clay soils can be problematic as DNA adsorbs to the clay particles and can thereby be preserved from lysed, non-viable cells for a substantial period of time. In order to accurately estimate the intact and living microbial community in the soil, extracellular DNA from dead, remnant bacterial cells needs to be removed prior to DNA extraction. One possibility is to use a sodium phosphate buffer to release both extracellular DNA and bacterial cells from the clay particles. After removing the extracellular DNA by centrifugation, the remaining viable cells can be harvested and DNA extracted. The described method is a modification of a procedure for separating extracellular DNA and bacterial cells from acidic clay soils.

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The modified method increases bacterial cell yields from acidic clay soils, such as acid sulfate soil.

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The modified method eliminates some steps from the original method, as only DNA from intact bacterial cells is required.

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The indirect DNA extraction method increases the workload compared to standard direct extraction methods, but subsequent downstream analyses will give a more representative picture of the viable microbial community composition in the soil.