Article pubs.acs.org/est
Metal(loid) Bioaccessibility Dictates Microbial Community Composition in Acid Sulfate Soil Horizons and Sulfidic Drain Sediments Jacqueline L. Stroud,*,† Adrian Low,‡ Richard N. Collins,† and Mike Manefield‡ †
Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia ‡ Centre for Marine Biofouling and Bioremediation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia S Supporting Information *
ABSTRACT: Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing. Diversity analyses were problematic due to the high microbiological heterogeneity between each geochemical replicate. Taxonomic analyses combined with measurements of metal(loid) bioaccessibility identified significant correlations to genera (5% phylogenetic distance) abundances. A number of positive correlations between genera abundance and bioaccessible metals concentrations were observed, indicating that metal(loid) tolerance influences microbial community compositions in these types of landscapes. Of note, Mn was highly bioaccessible (≤24% total soil Mn); and Mn bioaccessibility positively correlated to Acidobacterium abundance, but negatively correlated to Holophaga abundance. Two unidentified archaeal genera belonging to Crenarchaeota were also correlated to bioaccessible Mn concentrations, suggesting these genera can exploit Mn redox chemistry.
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INTRODUCTION Coastal acid sulfate soils are found over 40 000 km2 in Australia alone; and an estimated 1 million km2 worldwide.1 These formerly waterlogged, sulfidic soils were disturbed through drainage, excavation or drought leading to the oxidation of the iron-sulfide minerals. This oxidation and associated acidification generates rain-induced acidic and metalliferous (Al, Fe, Mn) soil groundwater discharge events which cause long-term river sterilization,1 the poisoning of aquifers,2 and threaten the Great Barrier Reef, Australia.3 The associated monosulfide formation in acid sulfate soil drainage channels is equally problematic, capable of deoxygenating aquatic ecosystems in seconds if disturbed.4 The treatment and management of acid sulfate soils costs $180 million per year in Queensland, Australia, alone, with costs incurred through the disruption to urban developments and the corrosion of infrastructure.5 No studies have characterized the microbial populations in acid sulfate soils which limits the opportunities for developing bioremediation technologies. The aim of this study was to characterize the microbial ecology of the soil horizons and drain sediments in order to improve the understanding of the biogeochemistry of these environments. Characterizing microbial communities (microbiomes) is reasonably routine via pyrosequencing analyses to determine taxonomic composition and abundance.6 Environmental factors © 2014 American Chemical Society
are linked to microbial community diversity, abundance and composition,7 for example, soil pH and microbial phyla are often correlated.8−10 It is well-known that total element concentrations have little relevance to the biologically available element pool. For example, poor correlations between element concentrations determined via open-tube digestion procedures and metal(loid) plant accumulation,11,12 or determined via harsh shake extraction techniques and microbial biodegradation extents.13,14 The bioaccessible pool of contaminants has been linked to microbial community function in organic contaminated environments,13−15 with bioaccessibility defined as the potential pool of chemical available to biological receptors, as opposed to bioavailable concentrations that are available at a specific point in time.16 We hypothesized that the labile inorganic element pool could be linked to microbial community abundance as a result of the acute selection pressures within acid sulfate landscapes. A number of chemical techniques are used to assess metal(loid) bioaccessibility in circum-neutral soils, for example diffusive gradient in thin films (DGT) or aqueous shake Received: Revised: Accepted: Published: 8514
March 30, 2014 June 29, 2014 July 7, 2014 July 7, 2014 dx.doi.org/10.1021/es501495s | Environ. Sci. Technol. 2014, 48, 8514−8521
Environmental Science & Technology
Article
Water gave satisfactory values within 90%) the community composition, with four common to all acid sulfate soil settings (Proteobacteria, Acidobacteria, Firmicutes, and Chlorof lexi), and Bacteriodetes as a major component of sulfidic drain sediments and Actinobacteria a major component of the acid sulfate soil field horizons. As unclassified OTU’s dominated the acid sulfate soil profile, the genus taxonomic resolution was used to compare and contrast the microbial ecology of this environment (SI Table 2a,b). Three genera, Acidobacterium, Holophaga, and Ornithinicoccus with >1% relative abundance were shared between the drain and soil settings (n = 12). A total of 29 genera were found in every soil sample (n = 9), which accounted for just 10−13% total genera identified, but dominated relative abundance (68−81%). The genus Sideroxydans was enriched in the sulfidic drain sediment, and declined in abundance from the topsoil to an absence in the transition zone in comparison to Chlorof lexus that was enriched in the soils. Only the drain sediments contained an abundance of Ferritrophicum, Gallionella, and Ferrovum in comparison to Leptospirillum and Alicyclobacillus that were only present in the transition zone. The abundance of Anaeromyxobacter was greater than Geobacter in the drain sediments, but the opposite trend was found for the soils and Geobacter abundance declined down the soil profile. The drain sediments also contained Geothrix, Pelobacter, and Acidiphilum which were absent from the soil horizons. Thiomonas was a highly abundant member of the drain sediment microbial community, but absent from the soils. The drain sediments also had higher diversity and abundance of Desulfobacterium and Desulfobacca, with just a low abundance of Desulfoglaeba found in the upper soil horizons, and Desulfomicrobium in the transition zone. Interestingly, Fodinicola, was increasingly enriched down the soil horizon, and was absent from the drain sediment. The genus Stella was abundant in all environments; Thermogemmatispora was absent in the drain sediments but increased in abundance down the soil profile where a concomitant reduction in Solibacter abundance was found. A total of 32 species (3% phylogenetic distance) were ubiquitous to at least one geochemical setting (SI Table 3). The drain sediments contained 2−19-fold more species than any soil layer. Total and Bioaccessible Metals in Acid Sulfate Soils and Sulfidic Sediments. Manganese was very highly
investigate relationships between genera abundance and environmental factors. For SI Table 2a, b, normalized bacteria genera abundance were ranked into five categories, top 5%, 5.1−10%, 10.1−25%, 25.1−50%, bottom > 50% abundance to reveal the constitutive microbial ecology within these geochemical settings.
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RESULTS Pyrosequencing. A total number of 100 800 raw reads were generated after pyrosequencing of which 63 691 quality sequences were generated after trimming. Rarefaction curves to determine pyrosequencing bacterial coverage were determined via OTUs identified at 3% phylogenetic distance using 693 sequences per replicate sample (based on the acid sulfate layer sample replicate 2 which had the fewest sequences, and also used for the inverse Simpson diversity index and AMOVA analyses). The coverage for the sulfidic drain sediments was 55 ± 0.1%, organic topsoil 72 ± 2%, the acid sulfate layer 78 ± 2% and transition zone 79 ± 7% (SI Figure 2). Diversity within Acid Sulfate Soils and Drain Sediments. Archaea were not detected by these methods in the drain sediments, bacterial diversity indices were used to assess diversity in this landscape (SI Figure 3). The inverse Simpson diversity index was significantly different (p < 0.001) within each geochemical grouping. For example, the diversity values for the drain sediment replicates (n = 3) ranged from 96−191. Grouping by geochemical setting revealed that the drain sediments were significantly more diverse than the soils with diversity values ranging between 28−58. The replicate samples significantly clustered within their geochemically defined grouping (Figure 1a) and an AMOVA identified that the microbial community between each geochemical grouping (n = 4) was significantly different (p < 0.001). Similarity in replicate OTUs (3% phylogenetic distance) differed within each geochemical grouping (Figure 1b), showing relatively low similarity to each other. The total number of OTUs (3% phylogenetic distance) varied between the drain sediment replicates varied by
