Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings

Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.National Institute of Environmental and Health Sciences (NIEHS) Superfund Research Program (SRP) [P42 ES004940]; National Science Foundation Graduate Research Fellowhip Program (NSF GRFP) [DGE-1143953]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Proteomics Analyses of the Opportunistic Pathogen Burkholderia vietnamiensis Using Protein Fractionations and Mass Spectrometry

The main objectives of this work were to obtain a more extensive coverage of the Burkholderia vietnamiensis proteome than previously reported and to identify virulence factors using tandem mass spectrometry. The proteome of B. vietnamiensis was precipitated into four fractions to as extracellular, intracellular, cell surface and cell wall proteins. Two different approaches were used to analyze the proteins. The first was a gel-based method where 1D SDS-PAGE was used for separation of the proteins prior to reverse phase liquid chromatography tandem mass spectrometry (LC-MS/MS). The second method used MudPIT analysis (Multi dimensional Protein Identification Technique), where proteins are digested and separated using cation exchange and reversed phase separations before the MS/MS analysis (LC/LC-MS/MS). Overall, gel-based LC-MS/MS analysis resulted in more protein identifications than the MudPIT analysis. Combination of the results lead to identification of more than 1200 proteins, approximately 16% of the proteins coded from the annotated genome of Burkholderia species. Several virulence factors were detected including flagellin, porin, peroxiredoxin and zinc proteases

Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF)

Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME pXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME pXRF. The FISH and ME pXRF images were aligned using Image.' software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49 +/- 0.19) than to bacteria (0.072 +/- 0.052) (p < 0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate. (C) 2016 Elsevier B.V. All rights reserved.National Institute of Environmental Health Sciences (NIEHS) Superfund Research Program (SRP) [P42 ES04940, R01 ES1709]; National Science Foundation Graduate Research Fellowhip Program (NSF GRFP) [DGE-1143953]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-765F00515]12 month embargo; published online: 29 September 2016This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.National Institute of Environmental and Health Sciences (NIEHS) Superfund Research Program (SRP) [P42 ES004940]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Phytotechnologies - Preventing Exposures, Improving Public Health

Phytotechnologies Have Potential to Reduce the Amount or Toxicity of Deleterious Chemicals and Agents, and Thereby, Can Reduce Human Exposures to Hazardous Substances. as Such, Phytotechnologies Are Tools for Primary Prevention in Public Health. Recent Research Demonstrates Phytotechnologies Can Be Uniquely Tailored for Effective Exposure Prevention in a Variety of Applications. in Addition to Exposure Prevention, Plants Can Be Used as Sensors to Identify Environmental Contamination and Potential Exposures. in This Paper, We Have Presented Applications and Research Developments in a Framework to Illustrate How Phytotechnologies Can Meet Basic Public Health Needs for Access to Clean Water, Air, and Food. Because Communities Can Often Integrate Plant-Based Technologies at Minimal Cost and with Low Infrastructure Needs, the Use of These Technologies Can Be Applied Broadly to Minimize Potential Contaminant Exposure and Improve Environmental Quality. These Natural Treatment Systems Also Provide Valuable Ecosystem Services to Communities and Society. in the Future, Integrating and Coordinating Phytotechnology Activities with Public Health Research Will Allow Technology Development Focused on Prevention of Environmental Exposures to Toxic Compounds. Hence, Phytotechnologies May Provide Sustainable Solutions to Environmental Exposure Challenges, Improving Public Health and Potentially Reducing the Burden of Disease. © 2013 Copyright Taylor and Francis Group, LLC

Surficial weathering of iron sulfide mine tailings under semi-arid climate

Mine wastes introduce anthropogenic weathering profiles to the critical zone that often remain unvegetated for decades after mining cessation. As such, they are vulnerable to wind and water dispersion of particulate matter to adjacent ecosystems and residential communities. In sulfide-rich ore tailings, propagation to depth of the oxidative weathering front controls the depth-variation in speciation of major and trace elements. Despite the prevalence of surficial mine waste deposits in arid regions of the globe, few prior studies have been conducted to resolve the near-surface profile of sulfide ore tailings weathered under semi-arid climate. We investigated relations between gossan oxidative reaction-front propagation and the molecular speciation of iron and sulfur in tailings subjected to weathering under semi-arid climate at an EPA Superfund Site in semi-arid central Arizona (USA). Here we report a multi-method data set combining wet chemical and synchrotron-based X-ray diffraction (XRD) and X-ray absorption near-edge spectroscopy (XANES) methods to resolve the tight coupling of iron (Fe) and sulfur (S) geochemical changes in the top 2 m of tailings. Despite nearly invariant Fe and S concentration with depth (130-140 and 100-120 g kg-1, respectively), a sharp redox gradient and distinct morphological change was observed within the top 0.5 m, associated with a progressive oxidative alteration of ferrous sulfides to (oxyhydr)oxides and (hydroxy)sulfates. Transformation is nearly complete in surficial samples. Trends in molecular-scale alteration were co-located with a decrease in pH from 7.3 to 2.3, and shifts in Fe and S lability as measured via chemical extraction. Initial weathering products, ferrihydrite and gypsum, transform to schwertmannite, then jarosite-group minerals with an accompanying decrease in pH. Interestingly, thermodynamically stable phases such as goethite and hematite were not detected in any samples, but ferrihydrite was observed even in the lowest pH samples, indicating its metastable persistence in these semiarid tailings. The resulting sharp geochemical speciation gradients in close proximity to the tailings surface have important implications for plant colonization, as well as mobility and bioavailability of co-associated toxic metal(loid)s.24 month embargo; published online: 5 June 2014This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt

Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt-soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth-dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.NSF [EAR-1344552, EAR-1340912, EAR-1417097]; Philecology Foundation of Fort Worth Texas; Water, Environmental, and Energy Solutions (WEES) initiative at the University of Arizona; office of Research, Discovery and Innovation's Accelerate for Success Grant at the University of Arizona; U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of Subsurface Biogeochemical Research Program's Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL); DOE [DE-AC06-76RLO 1830]6 month embargo; first published 28 March 2019.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Abundance and Activity of 16S rRNA, AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings

Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings.This research was supported by Grants P42 ES04940 and R01 ES017079 from the National Institute of Environmental Health Sciences Superfund Research Program, NIH (USA).12 month embargo; published online: 13 Dec 2014.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]