From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization
Journal Article Li, Xiaofang ; Bond, Philip L. ; Van Nostrand, Joy D. ; ... - Scientific Reports
Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil solublemore » Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera [typically Nocardioides and Altererythrobacter] were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes.« less
Cited by 30
- //doi.org/10.1038/srep12978
- Full Text Available
Plant Growth-Promoting Bacteria for Phytostabilization of Mine Tailings
Journal Article Grandlic, C J ; Mendez, M O ; Chorover, J ; ... - Environ. Sci. Tech. 42:2079,2008
Eolian dispersion of mine tailings in arid and semiarid environments is an emerging global issue for which economical remediation alternatives are needed. Phytostabilization, the revegetation of these sites with native plants, is one such alternative. Revegetation often requires the addition of bulky amendments such as compost which greatly increases cost. We report the use of plant growth-promoting bacteria [PGPB] to enhance the revegetation of mine tailings and minimize the need for compost amendment. Twenty promising PGPB isolates were used as seed inoculants in a series of greenhouse studies to examine revegetation of an extremely acidic, high metal content tailings samplemore » previously shown to require 15% compost amendment for normal plant growth. Several isolates significantly enhanced growth of two native species, quailbush and buffalo grass, in tailings. In this study, PGPB/compost outcomes were plant specific; for quailbush, PGPB were most effective in combination with 10% compost addition while for buffalo grass, PGPB enhanced growth in the complete absence of compost. Results indicate that selected PGPB can improve plant establishment and reduce the need for compost amendment. Further, PGPB activities necessary for aiding plant growth in mine tailings likely include tolerance to acidic pH and metals.« less
Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs
Journal Article Beam, Jacob P. ; Bernstein, Hans C. ; Jay, Zackary J. ; ... - Frontiers in Microbiology
Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park [YNP, WY, USA], and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe[III]-oxide mat ecosystems. Spatial and temporal changes in Fe[III]-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs [pH = 3-3.5; temperature = 68-75°C] inmore » YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages [4-40 days], and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14-30 days, corresponding to visible Fe[III]-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe[III]-oxide mats [1-2 cm thick]. First-order rate constants of Fe[III]-oxide accretion ranged from 0.046 to 0.05 day -1 , and in situ microelectrode measurements showed that the oxidation of Fe[II] is limited by the diffusion of O2 into the Fe[III]-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe[III]-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe[III]-oxide mats are also useful for understanding other Fe[II]-oxidizing systems.« less
Cited by 19
- //doi.org/10.3389/fmicb.2016.00025
- Full Text Available
Impact of water column acidification on protozoan bacterivory at the lake sediment-water interface
Journal Article Tremaine, S C ; Mills, A L - Applied and Environmental Microbiology; [United States]
Although the impact of acidification on planktonic grazer food webs has been extensively studied, little is known about microbial food webs either in the water column or in the sediments. Protozoan-bacterium interactions were investigated in a chronically acidified [acid mine drainage] portion of a lake in Virginia. The authors determined the distribution, abundance, apparent specific grazing rate, and growth rate of protozoa over a pH range of 3.6 to 6.5. Protozoan abundance was lower at the most acidified site, while abundance, in general, was high compared with other systems. Specific grazing rates were uncorrelated with pH and ranged between 0.02more » and 0.23 h{sup {minus}1}, values similar to those in unacidified systems. The protozoan community from an acidified station was not better adapted to low-pH conditions than a community from an unacidified site [multivariate analysis of variance on growth rates for each community incubated at pHs 4, 5, and 6]. Both communities had significantly lower growth rates at pHs 4 and 5 than at pH 6. Reduced protozoan growth rates coupled with high grazing rates and relatively higher bacterial yields [ratio of bacterial-protozoan standing stock] at low pH indicate reduced net protozoan growth efficiency and a metabolic cost of acidification to the protozoan community. However, the presence of an abundant, neutrophilic protozoan community and high bacterial grazing rates indicates that acidification of Lake Anna has not inhibited the bacterium-protozoan link of the sediment microbial food web.« less
Proteogenomic Approaches for the Molecular Characterization of Natural Microbial Communities
Journal Article Banfield, Jillian F. ; Verberkmoes, Nathan C ; Hettich, Robert ; ... - OMICS: A Journal of Integrative Biology
At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that themore » metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite [FeS2] dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry [MS]-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage [AMD]. AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.