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Open Rojas Dissertation Oct1 2013 The Pennsylvania State University The Graduate School Department of Ecosystem Science and Management EFFECT OF VEGETATIVE RECLAMATION ON MICROBIAL DIVERSITY AND IRON BIOGEOCHEMISTRY IN ACID MINE DRAINAGE PRECIPITATES AT A 50-YR-OLD BARRENS A Dissertation in Soil Science and Biogeochemistry by Claudia Macarena Rojas Alvarado © 2013 Claudia Macarena Rojas Alvarado Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2013 The dissertation of Claudia Macarena Rojas Alvarado was reviewed and approved* by the following: Mary Ann Bruns Associate Professor of Soil Microbiology Dissertation Co-Advisor Co-Chair of Committee Carmen E. Martínez Associate Professor of Environmental Soil Chemistry Dissertation Co-Advisor Co-Chair of Committee Patrick Drohan Associate Professor of Pedology Sridhar Komarneni Distinguished Professor of Clay Mineralogy Rachel A. Brennan Associate Professor of Environmental Engineering John E. Watson Professor of Soil Physics Graduate Program Head for the Department of Ecosystem Sciences and Management *Signatures are on file in the Graduate School iii ABSTRACT Acid mine drainage (AMD) barrens result from the death of vegetation resulting from overland flow of acidic metal-rich waters emerging from abandoned underground mines. As acidic waters flow overland, oxidation and hydrolysis reactions result in accumulation of ferric iron (oxy) hydroxide precipitates on soil surfaces. AMD barrens can become a source of further pollution if exposed acidic precipitates are not protected against surface runoff. In 2006, a restoration experiment was conducted by our research group at a 50-year-old AMD barrens to determine whether vegetation could be established by altering, rather than removing, surface layers of acidic iron-rich precipitates at the site which is representative of other mining-degraded areas. In that study, three zones were distinguished by thickness and color of precipitate surface layers and by moisture content as influenced by depth to fragipan layers in underlying native soils. Acidic precipitates in experimental plots were amended in place by a one- time incorporation of lime and compost (top 15 cm) and a first-year oats nurse crop to improve growth of a sown reclamation seed mixture. Plant composition in the first, second, and fourth growing season consisted mainly of oats, sown species, and indigenous species, respectively. In all three zones, plots that received compost had greater than 70% vegetative cover at the end of the fourth growing season. The research presented in this dissertation builds on the investigation initiated in 2006 in the zone where subsurface AMD flow was most shallow and focuses on non- reclaimed (control) precipitates covered by mossy biological crusts and reclaimed precipitates sustaining vegetation. Iron (Fe) biogeochemistry in AMD precipitates was studied to gain an understanding of potential losses of redox-active metals after plant-based reclamation. As mobility of redox-active metals can be increased by enhanced microbial activity in the rooting zones of growing plants, we iv compared the forms of Fe in the reclaimed and control precipitates five years post-reclamation. Since Fe is the most abundant metal in many mine drainages, root exudation by growing plants could stimulate Fe(III)-reducing activity in rhizospheres, resulting in losses of soluble Fe(II) from the system. Precipitates were sampled from moist yet unsaturated surface sections (8-cm depth) excised from replicate plots. Four precipitate types, reclaimed root-adhering (RR); reclaimed below-roots (RB); control crust-adhering (CC); and control below-crust (CB) were obtained before selective-extraction analyses and microbial counts were performed. Reclaimed and control precipitates had mean Fe contents of 454 and 690 g kg-1, respectively. Ferrozine tests of extracts indicated that Fe(II) concentrations were three- to five-fold higher in reclaimed precipitates than in control precipitates. Organically bound Fe and amorphous iron oxides, as fractions of total Fe, were also higher in reclaimed than in control precipitates. Estimates of Fe-reducing and Fe- oxidizing bacteria were four- to tenfold higher in root-adherent precipitates than in both types of control precipitates, indicating a potential for increased Fe cycling in plant rhizospheres. Scaling up Fe measurements from experimental plots suggested that potential total Fe losses during the 5- yr period following reclamation were 45 t Fe ha-1 yr-1. Microbial communities inhabiting AMD-impacted environments have been more extensively studied in aqueous rather than terrestrial systems. Our reclamation study provided the opportunity to gain insights into AMD-derived bacterial and eukaryotic communities in unsaturated, edaphic habitats. Precipitates of the same types as described for the Fe-biochemistry study (RR, RB, CC, and CB) were collected six years post-reclamation. At the time of sampling, all four precipitate types had similar pH levels (2.5-2.7) because reclaimed precipitates had gradually become more acidic following the one-time lime application in 2006. Bacterial and eukaryotic diversity were assessed using 454 pyrosequencing of 16S rRNA (V1-V3/V5 region) v and the 18S rRNA (V4-V5 region) genes. Contrary to our projections we observed high bacterial and eukaryotic diversity across all samples. For bacterial libraries, we recovered a total of 3,150 operational taxonomic units (OTUs) at 97% similarity. Approximately 50% of these were exclusively found in reclaimed precipitates (RR, RB or both), 33% were unique to control precipitates (CC, CB, or both), and 6% were shared among the four precipitate types. Nineteen phyla were identified in the four type of precipitates and 13 of these were found in all samples. Proteobacteria comprised the most abundant representatives in reclaimed precipitates while Acidobacteria were more abundant in root-and crust-adherent precipitates. The latter sample also showed the highest abundance of Actinobacteria. The bacterial composition of incipient soils developed from AMD did not resemble those typically described for aquatic AMD systems. Among the classical AMD bacteria, only Leptospirillum ferriphilum, Leptospirillum ferrodiazotrophum, and Acidiphilium cryptum were detected in our study but at a very low frequency (≤ 0.1% ). Eukaryotic diversity was also higher in reclaimed precipitates than in control precipitates, reflecting the positive influence of plant establishment. Of the total 494 OTUs identified at the 95% similarity level, about 62% were found exclusively in reclaimed precipitates (RR, RB or both), 20% were unique to control precipitates (CC, CB, or both), and only 7% were shared among the four precipitate types. Since libraries from control precipitates were dominated by bryophyte sequences, these and other macroeukaryotic sequences were removed before calculating the percentages of microeukaryotic taxa in each precipitate. The main microeukaryotic taxa identified in reclaimed precipitates were Basidiomycota, 48% in RR and 39% in RB. In contrast, Ascomycota were more abundant in control precipitates, 50% in CC and 18% in CB, reflecting a shift in fungal community composition following reclamation. Many taxa vi reported to be abundant in water-impacted AMD habitats were either very low in abundance or not detected. These studies demonstrate how acidic precipitates containing redox-active metals respond to plant establishment in hydrologically sensitive environments and increase our knowledge of the microbial biodiversity in AMD impacted terrestrial environments. In addition, these findings help to identify microbial taxa that reflect development of edaphic habitats which could be indicative of reclamation success and restoration of soil ecosystem functions. vii TABLE OF CONTENTS List of Figures .......................................................................................................................... ix List of Tables ............................................................................................................................ xi ACKNOWLEDGEMENTS ..................................................................................................... xiii! Chapter 1 Introduction ............................................................................................................. 1! Formation of Acid Mine Drainage ................................................................................... 1! Genesis and Chemistry of Acid Mine Drainage Precipitates ........................................... 2! Microorganisms associated with AMD systems .............................................................. 3! AMD Impacts and Environmental Implications .............................................................. 8! Research site ..................................................................................................................... 10! Dissertation organization and objectives .......................................................................... 13! References ........................................................................................................................ 16! Chapter 2 Fe biogeochemistry in reclaimed acid mine drainage precipitates—implications for phytoremediation ........................................................................................................ 20! Introduction .....................................................................................................................
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