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Microbiology of boreal acid sulfate soils: Biogeochemical drivers of acidity generation and metals leaching
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. (Ctr Ecol & Evolut Microbial Model Syst EEMiS)ORCID iD: 0000-0003-2943-5158
2024 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Acid sulfate soils are described as the nastiest soils on Earth and are broadly composed of metal sulfides. These minerals are mostly harmless in a reducing environment. However, when these soils are drained oxygen infiltration occurs. Oxidation initiates a geochemical process, thereby starting the generation of acidity. As the pH drops, a consortium of acidophilic microbiota begin to grow and flourish. These microbes catalyze the oxidation reactions, which further generates acidity, thus driving the pH even lower. The decreasing pH leads to the solubilization of any co-occurring metals within the system. During flushing events the built-up acidity and solubilized metals mobilize and flow out of the soils into surrounding waterways to the potentially lethal detriment of resident flora and fauna.

This dissertation firstly explores the microbial communities that inhabit acid sulfate soils throughout Sweden and around Vaasa, Finland, and secondly the analogous communities of a mine waste rock repository in northern Sweden. Results from Finland showed an increase in relative abundances of extremely acidophilic microbes correlated to the decreasing pH values that followed the oxidation front. Acidity generation was not mitigated by additions of lime. Further laboratory incubations found that higher volumes and finer material sizes of lime delayed acid generation but did not prevent the development of neutrophilic iron and sulfur oxidizing microbes. The survey of Sweden extended the distribution range of acid sulfate soils and found community differences between the northerly and southerly acid sulfate soils, which were hypothesized to be a result of regional temperature variation. Furthermore, regional differences of the field oxidized samples disappeared following laboratory incubations, further supporting temperature as a driver of regional differences. Lastly, the Swedish waste rock repository study suggested that there were tipping points associated with ongoing oxidation. Subsurface associated communities rapidly decreased following excavation and were slowly replaced by a simple acidophilic community; over time a radiation of acidophiles occurred leading to an increase in acidophile diversity.

These studies together show that metal sulfide rich environments are host to resident neutrophilic to extreme acidophilic microbial communities that play integral roles to the generation of acidity and metals leaching. The composition of those communities differ based on temperature, pH, substrate type, and oxidation age. With regard to remediation strategy development, the application of fine grained lime in combination with peat may hold potential to for short termed acidity mitigation. However cautionis required when transitioning from laboratory based approaches to field trials as the communities are dynamic and complex. 

Place, publisher, year, edition, pages
Växjö: Linnaeus University Press, 2024. , p. 49
Series
Linnaeus University Dissertations ; 541
Keywords [en]
Acid sulfate soils, acid rock drainage, microbial ecology, acidophiles, oxidation, sediments, 16S rRNA gene sequences
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology
Identifiers
URN: urn:nbn:se:lnu:diva-132271DOI: 10.15626/LUD.541.2024ISBN: 9789180821995 (print)ISBN: 9789180822008 (electronic)OAI: oai:DiVA.org:lnu-132271DiVA, id: diva2:1895656
Public defence
2024-10-11, Fullriggaren, Ma135K, Pedalstråket 7, Kalmar, 09:00 (English)
Opponent
Supervisors
Available from: 2024-09-16 Created: 2024-09-06 Last updated: 2025-05-05Bibliographically approved
List of papers
1. Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials
Open this publication in new window or tab >>Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials
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2022 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 813, article id 151864Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2022
Keywords
Pyrite, Iron, Mitigation, Acidophile, Oxidation, 16S rRNA gene
National Category
Environmental Sciences Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-111111 (URN)10.1016/j.scitotenv.2021.151864 (DOI)000767232600018 ()34822903 (PubMedID)2-s2.0-85120412916 (Scopus ID)2022 (Local ID)2022 (Archive number)2022 (OAI)
Available from: 2022-04-07 Created: 2022-04-07 Last updated: 2024-09-06Bibliographically approved
2. A nationwide acid sulfate soil study: A rapid and cost-efficient approach for characterizing large-scale features
Open this publication in new window or tab >>A nationwide acid sulfate soil study: A rapid and cost-efficient approach for characterizing large-scale features
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2023 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 869, article id 161845Article in journal (Refereed) Published
Abstract [en]

Acid sulfate soils are sulfide-rich soils that pose a notable environmental risk as their strong acidity and low pH mobilizes metals from soil minerals leading to both acidification and metal contamination of the surrounding environment. In this study a rapid and cost-efficient approach was developed to resolve the main distribution patterns and geochemical features of acid sulfate soils throughout coastal plains stretching for some 2000 km in eastern, southern, and western Sweden. Of the investigated 126 field sites, 47 % had acid sulfate soils including 33 % active, 12 % potential, and 2 % pseudo acid sulfate soils. There were large regional variations in the extent of acid sulfate soils, with overall much higher proportions of these soils along the eastern coastal plains facing the Baltic Sea than the western coastal plains facing the Kattegatt/Skagerrak (Atlantic Ocean). The sulfur concentrations of the soil's parent material, consisting of reduced near-pH neutral sediments, were correlated inversely both with the minimum pH of the soils in situ (rS = −0.65) and the pH after incubation (oxidation) of the reduced sediments (rS = −0.77). This indicated the importance of sulfide levels in terms of both present and potential future acidification. Hence, the higher proportion of acid sulfate soils in the east was largely the result of higher sulfur concentrations in this part of the country. The study showed that the approach was successful in identifying large-scale spatial patterns and geochemical characteristics of importance for environmental assessments related to these environmentally unfriendly soils.

Place, publisher, year, edition, pages
Elsevier, 2023
National Category
Soil Science
Research subject
Natural Science, Environmental Science
Identifiers
urn:nbn:se:lnu:diva-119131 (URN)10.1016/j.scitotenv.2023.161845 (DOI)000925436800001 ()36709904 (PubMedID)2-s2.0-85147197802 (Scopus ID)
Funder
Swedish Environmental Protection Agency
Available from: 2023-02-07 Created: 2023-02-07 Last updated: 2025-02-05Bibliographically approved
3. Regional variation in Swedish acid sulfate soil microbial communities is influenced by temperature and geochemistry
Open this publication in new window or tab >>Regional variation in Swedish acid sulfate soil microbial communities is influenced by temperature and geochemistry
2024 (English)In: European Journal of Soil Science, ISSN 1351-0754, E-ISSN 1365-2389, Vol. 75, no 1, article id e13452Article in journal (Refereed) Published
Abstract [en]

Acid sulfate soils are frequently described as the nastiest soils on Earth, and they pose environmental risks associated with their strong acidity and consequential mobilization of toxic metals present in the soils. Within Sweden, acid sulfate soils have been extensively studied around the northern Baltic coastline and have now been found to occur throughout the area below the maximum Holocene marine limit that stretches for some 2000 km from North to South. This study investigated 20 active acid sulfate soils (field tested pH < 4.0) collected throughout this area that were tested for microbial community composition using 16S rRNA gene amplicons, representing a novel study of microbial communities in ripening zones across a broad regional scale. The microbial community compositions exhibited a north (boreal zone) to south (hemiboreal zone) regional divide, primarily within the oxidized zone (pH < 4.0), to a lesser degree in the transition zone (steep pH gradient), while little differences were observed in the reduced zone (near-neutral pH). For instance, a higher relative abundance of Ktedonobacteraceae was identified in the northern boreal and Gallionellaceae in the southern hemiboreal oxidized zones. In addition, microbial taxa associated with iron and sulphur oxidation and reduction were identified, such as Acidobacteriaceae, Gallionellaceae and Koribacteraceae that have been previously identified in other acid sulfate soils and acid mine drainage settings. The predominant controls of the microbial community differences were the north-south divide indicative of a strong soil-temperature effect followed by soil zones suggesting an influence of the soils' pH and/or redox conditions.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
16S rRNA gene amplicons, acidophile, boreal, iron, pH
National Category
Microbiology Soil Science Geochemistry
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-127378 (URN)10.1111/ejss.13452 (DOI)001145568200001 ()2-s2.0-85182625354 (Scopus ID)
Available from: 2024-02-01 Created: 2024-02-01 Last updated: 2025-04-10Bibliographically approved
4. Swedish Hypersulfidic Soil Material Incubations Suggest Temperature Mainly Drives Regional Microbial Community Variation
Open this publication in new window or tab >>Swedish Hypersulfidic Soil Material Incubations Suggest Temperature Mainly Drives Regional Microbial Community Variation
2025 (English)In: European Journal of Soil Science, ISSN 1351-0754, E-ISSN 1365-2389, Vol. 76, no 2, article id e70106Article in journal (Refereed) Published
Abstract [en]

Acid sulfate soils impact surrounding ecosystems with pronounced environmental damage via leaching of strong acidity along with the concurrent mobilization of toxic metals present in the soils and, in consequence, they are often described as the nastiest soils on Earth. Within Sweden, acid sulfate soils are distributed mainly under the maximum Holocene marine limit that stretches the length of the country, some 2000 km north to south. Despite only minor geographical differences in the geochemical composition of the Swedish acid sulfate soils, their field oxidation zone microbial community compositions differ along a north-south regional divide. This study compared the 16S rRNA gene amplicon-based microbial community compositions of field oxidation zones (field tested pH _ 4.0) with reduced zone samples (field tested pH _ 6.5) collected from the same field sites throughout Sweden that had acidified (final pH _ 4.0) after laboratory incubation at approximately 20 degrees C. The previously identified regional differences observed in field oxidation zone microbial compositions were notably absent in the laboratory incubation samples. Instead, a commonly shared community was selected for with few statistically significant differences regardless of regional origin. For instance, the potential eurypsychrophilic Baltobacteraceae family was found in higher relative abundances in the northerly region of the field oxidation zone samples than the southern regions and was notably absent from the laboratory incubation samples. Furthermore, the microbial communities of the laboratory incubation samples were dominated by acidophilic autotrophic Acidithiobacillaceae and chemoheterotrophic Rhodanobacteraceae and Burkholderiaceae that have optimal growth temperatures (_= 20 degrees C) greater than what was experienced by the field oxidation zone samples when sampled (similar to 2 degrees C-9 degrees C). These data suggested that in the absence of significant geochemical differences, temperature was the predominant driver of microbial community composition in Swedish acid sulfate soil materials.

Place, publisher, year, edition, pages
Wiley, 2025
Keywords
16S rRNA gene amplicons, acid sulfate soils, iron, microbial diversity, oxidation, sulfur
National Category
Microbiology Soil Science
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-138206 (URN)10.1111/ejss.70106 (DOI)001468130800001 ()
Available from: 2025-04-29 Created: 2025-04-29 Last updated: 2025-05-05
5. Geochemical and microbial responses to limestone and peat treatment of incubated hypermonosulfidic sediments
Open this publication in new window or tab >>Geochemical and microbial responses to limestone and peat treatment of incubated hypermonosulfidic sediments
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2025 (English)In: European Journal of Soil Science, ISSN 1351-0754, E-ISSN 1365-2389, Vol. 76, no 1, article id e70024Article in journal (Refereed) Published
Abstract [en]

Fine-grained hypermonosulfidic sediments are widespread on the coastal plains of the northern Baltic Sea that when drained, cause the formation and dispersion of acid and toxic-metal species. In this study, a 30-month laboratory oxidation experiment with such a sediment was performed in incubation cells. To minimize or prevent acidification, limestone was applied in two grain sizes: agricultural limestone with particles that were all <3.15 mm and half of them <0.80 mm, and fine-grained limestone with a median grain size of 2.5 mu m. The amount of limestone applied corresponded to the theoretical acidity contained in the sulfides, as well as four times that amount. Another treatment included addition of peat to the low limestone dose to test its effects on immobilizing sufhur and metals. The pH of the drainage water and solid phase decreased to pH <4.0 in the control, and to pH <5.0 in the coarse-grained low-limestone treatment, but remained near-neutral in the other treatments. Hence, the fine-grained limestone effectively hindered acidity formation in contrast with the coarse-grained limestone when applied in amounts corresponding to the potential acidity held in the sulfides. The limestone treatments further overall decreased the rate of pyrite oxidation, slowed down the movement of the oxidation front, strongly minimized the formation of dissolved and solid-phase labile Al, and caused formation of gypsum as well as more labile secondary Fe(III) phases than corresponding Fe phases formed in the control. The limestone and peat treatments also caused shifts in the 16S rRNA gene-based microbial communities, where the control developed acidophilic iron and sulfur oxidizing communities that promoted acidity and metal release. Instead, the limestone-treated unacidified incubations developed acid tolerance to neutrophilic communities of iron and sulfur oxidizers that promoted sulfate formation without acidity release. The results showed that limestone treatments have several biogeochemical effects, and that using a fine-grained limestone as amendment was favourable in terms of minimizing acidity formation and metal release.

Place, publisher, year, edition, pages
John Wiley & Sons, 2025
Keywords
acidity, iron monosulfides, limestone, sediments, sulfur, treatments
National Category
Geochemistry Microbiology
Research subject
Environmental Science, Environmental Chemistry; Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-134446 (URN)10.1111/ejss.70024 (DOI)001385620600001 ()2-s2.0-85213529030 (Scopus ID)
Available from: 2025-01-14 Created: 2025-01-14 Last updated: 2025-05-05Bibliographically approved
6. Sulfidic mine waste rock alkaliphilic microbial communities rapidly replaced by aerobic acidophiles following deposition
Open this publication in new window or tab >>Sulfidic mine waste rock alkaliphilic microbial communities rapidly replaced by aerobic acidophiles following deposition
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2024 (English)In: Biogeochemistry, ISSN 0168-2563, E-ISSN 1573-515X, Vol. 168, no 1, article id 9Article in journal (Refereed) Published
Abstract [en]

The increased mining of metals required to meet future demands also generates vast amounts of waste rock that depending on the ore, can contain substantial amounts of metal sulfides. Unconstrained storage of these mining biproducts results in the release of acidic metal laden effluent (termed 'acid rock drainage') that causes serious damage to recipient ecosystems. This study investigated the development of 16S rRNA gene based microbial communities and physiochemical characteristics over two sampling occasions in three age classes of rock, from newly mined to > 10 years in a boreal metal sulfide waste repository. Analysis of the waste rocks showed a pH decrease from the youngest to oldest aged waste rock suggesting the development of acid rock leachate. The microbial communities differed between the young, mid, and old samples with increasing Shannon's H diversity with rock age. This was reflected by the young age microbial community beta diversity shifting towards the mid aged samples suggesting the development of a community adapted to the low temperature and acidic conditions. This community shift was characterized by the development of iron and sulfur oxidizing acidophilic populations that likely catalyzed the dissolution of the metal sulfides. In conclusion, the study showed three potential microbial community transitions from anaerobic species adapted to underground conditions, through an aerobic acidophilic community, to a more diverse acidophilic community. This study can assist in understanding acid rock drainage generation and inform on strategies to mitigate metal and acid release.

Place, publisher, year, edition, pages
Springer, 2024
Keywords
16S rRNA gene amplicons, Acid rock drainage, Heavy metals, Microbial diversity, Psychrophile
National Category
Microbiology Geochemistry
Research subject
Ecology, Microbiology; Environmental Science, Environmental Chemistry
Identifiers
urn:nbn:se:lnu:diva-134447 (URN)10.1007/s10533-024-01198-0 (DOI)001389021700001 ()2-s2.0-85213697310 (Scopus ID)
Available from: 2025-01-14 Created: 2025-01-14 Last updated: 2025-05-05Bibliographically approved

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