Journal articles: 'Microbe-mineral Interaction'

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OLSSON-FRANCIS, K., R. VAN HOUDT, M. MERGEAY, N. LEYS, and C. S. COCKELL. "Microarray analysis of a microbe-mineral interaction." Geobiology 8, no. 5 (August 15, 2010): 446–56. http://dx.doi.org/10.1111/j.1472-4669.2010.00253.x.

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Cuadros, Javier. "Clay minerals interaction with microorganisms: a review." Clay Minerals 52, no. 2 (June 2017): 235–61. http://dx.doi.org/10.1180/claymin.2017.052.2.05.

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AbstractInterest in mineral–microbe interaction has grown enormously over recent decades, providing information in a puzzle-like manner which points towards an ever increasingly intimate relationship between the two; a relationship that can be truly termed co-evolution. Clay minerals play a very central role in this co-evolving system. Some 20 years ago, clay scientists looked at clay mineral–microbe studies as a peripheral interest only. Now, can clay scientists think that they understand the formation of clay minerals throughout geological history if they do not include life in their models? The answer is probably no, but we do not yet know the relative weight of biological and inorganic factors involved in driving clay-mineral formation and transformation. Similarly, microbiologists are missing out important information if they do not investigate the influence and modifications that minerals, particularly clay minerals, have on microbial activity and evolution. This review attempts to describe the several points relating clay minerals and microorganisms that have been discovered so far. The information obtained is still very incomplete and many opportunities exist for clay scientists to help to write the real history of the biosphere.

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Xia, Jin Lan, Hong Chang Liu, Zhen Yuan Nie, Hong Rui Zhu, Yun Yang, Lei Wang, Jian Jun Song, et al. "Characterization of Microbe-Mineral Interfacial Interaction Based on Synchrotron Radiation Techniques." Advanced Materials Research 1130 (November 2015): 123–26. http://dx.doi.org/10.4028/www.scientific.net/amr.1130.123.

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This article presents the progress on characterization of the interfacial interaction between sulfur oxidizing microbes and sulfide minerals by using of synchrotron radiation-based techniques including S/Fe/Cu X-ray absorption near-edge structure spectroscopy (XANES), X-ray Diffraction (XRD), micro-X-ray fluorescence (μ-XRF) mapping and micro-scanning transmission X-ray microscopy (μ-STXM) imaging, together with other accessory approaches such as SEM/EDS, Raman spectroscopy, FT-IR spectroscopy, and electrochemical methods as well as comparative proteomics methodology.

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Mhonde, Ngoni, Mariette Smart, Kirsten Corin, and Nora Schreithofer. "Investigating the Electrochemical Interaction of a Thiol Collector with Chalcopyrite and Galena in the Presence of a Mixed Microbial Community." Minerals 10, no. 6 (June 19, 2020): 553. http://dx.doi.org/10.3390/min10060553.

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High microbial cell counts have been recorded in sewage waters employed as process water in mineral beneficiation plants across the world. The presence of these microbes can negatively impact flotation performance through mineral passivation, although some microbes improve flotation performance as investigated in various bio-flotation studies. The current study aims to understand the electrochemical behaviour of minerals in the presence of a sodium ethyl xanthate (SEX) collector and microbes originating from a sulphide ore processing plant in South Africa. The electrochemical response was correlated to observe flotation performance. Mixed potential measurements were conducted in parallel to microflotation tests, to assess the hydrophilicity or hydrophobicity induced on sulphide minerals adapted to microbe-laden synthetic plant water. Sulphide minerals’ mixed potentials and interactions of SEX with sulphide minerals were dramatically reduced in the presence of the mixed microbial community (MMC). The observations were correlated with poor flotation efficacy noted in microflotation tests. These fundamental results shed light on how the adsorption of thiol collectors on sulphide minerals is adversely affected by microbes, prompting a discussion on flotation process monitoring when mineral beneficiation is conducted using microbe-laden water.

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Breier, J. A., S. N. White, and C. R. German. "Mineral–microbe interactions in deep-sea hydrothermal systems: a challenge for Raman spectroscopy." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1922 (July 13, 2010): 3067–86. http://dx.doi.org/10.1098/rsta.2010.0024.

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In deep-sea hydrothermal environments, steep chemical and thermal gradients, rapid and turbulent mixing and biologic processes produce a multitude of diverse mineral phases and foster the growth of a variety of chemosynthetic micro-organisms. Many of these microbial species are associated with specific mineral phases, and the interaction of mineral and microbial processes are of only recently recognized importance in several areas of hydrothermal research. Many submarine hydrothermal mineral phases form during kinetically limited reactions and are either metastable or are only thermodynamically stable under in situ conditions. Laser Raman spectroscopy is well suited to mineral speciation measurements in the deep sea in many ways, and sea-going Raman systems have been built and used to make a variety of in situ measurements. However, the full potential of this technique for hydrothermal science has yet to be realized. In this focused review, we summarize both the need for in situ mineral speciation measurements in hydrothermal research and the development of sea-going Raman systems to date; we describe the rationale for further development of a small, low-cost sea-going Raman system optimized for mineral identification that incorporates a fluorescence-minimizing design; and we present three experimental applications that such a tool would enable.

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Hochella, M. F. "Sustaining Earth: Thoughts on the present and future roles of mineralogy in environmental science." Mineralogical Magazine 66, no. 5 (October 2002): 627–52. http://dx.doi.org/10.1180/0026461026650053.

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AbstractSustaining Earth, in the face of both technology thrusts and population dynamics, depends on our ability to maintain a delicate balance between human-promoted planetary modification and decline thresholds for land (soils), water, atmosphere, and biological systems. Mineralogy, as much as any other single science, will be central to this process. A set of links between Earth sustainability issues and the science of mineralogy are formulated and discussed in this discourse. The strongest ties exist in the areas of mineral-water and mineral-atmosphere interactions. Minerals are also particularly important in human disease generation. In addition, due to the role of minerals as invaluable economic resources, the environmental consequences of mining also come into play. New subdisciplines have recently emerged to bring mineralogy even closer to Earth sustainability issues, particularly mineral-microbe interaction science and nanomineralogy

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Yang, Kiho, Hanbeom Park, and Jinwook Kim. "Application of Electron Energy Loss Spectroscopy - Spectrum Imaging (EELS-SI) for Microbe-mineral Interaction." Journal of the mineralogical society of korea 32, no. 1 (March 31, 2019): 63–69. http://dx.doi.org/10.9727/jmsk.2019.32.1.63.

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Sanyal, Santonu Kumar, and Jeremiah Shuster. "Gold particle geomicrobiology: Using viable bacteria as a model for understanding microbe–mineral interactions." Mineralogical Magazine 85, no. 1 (February 2021): 117–24. http://dx.doi.org/10.1180/mgm.2021.19.

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AbstractThe biogeochemical cycling of gold has been proposed from studies focusing on gold particle morphology, surface textures and associated bacteria living on the surface of gold particles. Additionally, it has been suggested that metabolically active bacteria on particles catalyse gold dissolution and gold re-precipitation processes, i.e. fluid–bacterial–mineral interaction within microenvironments surrounding particles. Therefore, the isolation and characterisation of viable bacteria from gold particles can be used as a model to improve the understanding of bacterial–gold interactions. In this study, classical microbiology methods were used to isolate a gold-tolerant bacterium (Acinetobacter sp. SK-43) directly from gold particles. The genome of this isolate contained diverse (laterally acquired) heavy-metal resistance genes and stress tolerance genes, suggesting that gene expression would confer resistance to a wide range of potentially toxic metals that could occur in the surrounding microenvironment. The presence of these genes, along with genes for nutrient cycling under nutrient-limited conditions highlights the genomic capacity of how Acinetobacter sp. SK-43 could survive on gold particles and remain viable. Laboratory experiments demonstrated that this isolate could grow in the presence of soluble gold up to 20 μM (AuCl3) and that >50% of soluble gold was reduced upon exposure. Collectively, these results suggest that Acinetobacter sp. SK-43 (and presumably similar bacteria) could survive the cytotoxic effects of soluble Au from particles undergoing dissolution. This study provides comprehensive insight on the possible bacterial contributions to gold biogeochemical cycling in natural environments.

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Xia, Jinlan, Hongchang Liu, Zhenyuan Nie, Xiaolu Fan, Duorui Zhang, Xingfu Zheng, Lizhu Liu, Xuan Pan, and Yuhang Zhou. "Taking insights into phenomics of microbe-mineral interaction in bioleaching and acid mine drainage: Concepts and methodology." Science of The Total Environment 729 (August 2020): 139005. http://dx.doi.org/10.1016/j.scitotenv.2020.139005.

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Susilawati, Dr Rita. "Bioremediation Experiment Using Hydrocarbon Degrading Bacteria." Jurnal Geologi dan Sumberdaya Mineral 20, no. 1 (February 4, 2019): 1. http://dx.doi.org/10.33332/jgsm.2019.v20.1.1-7.

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A laboratory experiment was set up to demonstrate the capability of microbe to remediate petroleum hydrocarbon contaminated beach sand. Oil contaminated soil was used as a source of inoculum for hydrocarbon degrading bacteria (HDB) while oil contaminated beach sand was used as remediation object. The growth of HDB in the inocula was enriched and stimulated through the addition of nutrient in the form of vitamin and mineral as well the addition of oil waste as a source of carbon. Experiment took place in the course of approximately five weeks. Microscopic observation clearly showed the interaction between microbe and oil contaminant both in enrichment and bioremediation samples. The result of the experiment also suggests that approximately 25% of the petroleum hydrocarbon mass in the contaminated beach sand was biodegraded over the course of one month. Overall, the results of this experiment suggest the potential of bioremediation method to treat petroleum hydrocarbon polluted environment.Keywords: bacteria, bioremediation, hydrocarbon

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Susilawati, Rita. "Bioremediation Experiment Using Hydrocarbon Degrading Bacteria." Jurnal Geologi dan Sumberdaya Mineral 20, no. 1 (February 4, 2019): 1. http://dx.doi.org/10.33332/jgsm.geologi.20.1.1-7.

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A laboratory experiment was set up to demonstrate the capability of microbe to remediate petroleum hydrocarbon contaminated beach sand. Oil contaminated soil was used as a source of inoculum for hydrocarbon degrading bacteria (HDB) while oil contaminated beach sand was used as remediation object. The growth of HDB in the inocula was enriched and stimulated through the addition of nutrient in the form of vitamin and mineral as well the addition of oil waste as a source of carbon. Experiment took place in the course of approximately five weeks. Microscopic observation clearly showed the interaction between microbe and oil contaminant both in enrichment and bioremediation samples. The result of the experiment also suggests that approximately 25% of the petroleum hydrocarbon mass in the contaminated beach sand was biodegraded over the course of one month. Overall, the results of this experiment suggest the potential of bioremediation method to treat petroleum hydrocarbon polluted environment.Keywords: bacteria, bioremediation, hydrocarbon DOI: 10.33332/jgsm.2019.v20.1.1-7

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Susilawati, Rita. "Bioremediation Experiment Using Hydrocarbon Degrading Bacteria." Jurnal Geologi dan Sumberdaya Mineral 20, no. 1 (February 4, 2019): 1. http://dx.doi.org/10.33332/jgsm.geologi.v20i1.335.

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A laboratory experiment was set up to demonstrate the capability of microbe to remediate petroleum hydrocarbon contaminated beach sand. Oil contaminated soil was used as a source of inoculum for hydrocarbon degrading bacteria (HDB) while oil contaminated beach sand was used as remediation object. The growth of HDB in the inocula was enriched and stimulated through the addition of nutrient in the form of vitamin and mineral as well the addition of oil waste as a source of carbon. Experiment took place in the course of approximately five weeks. Microscopic observation clearly showed the interaction between microbe and oil contaminant both in enrichment and bioremediation samples. The result of the experiment also suggests that approximately 25% of the petroleum hydrocarbon mass in the contaminated beach sand was biodegraded over the course of one month. Overall, the results of this experiment suggest the potential of bioremediation method to treat petroleum hydrocarbon polluted environment.Keywords: bacteria, bioremediation, hydrocarbon DOI: 10.33332/jgsm.2019.v20.1.1-7

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Susilawati, Dr Rita. "Bioremediation Experiment Using Hydrocarbon Degrading Bacteria." Jurnal Geologi dan Sumberdaya Mineral 20, no. 1 (February 4, 2019): 1. http://dx.doi.org/10.33332/jgsm.v20i1.335.

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A laboratory experiment was set up to demonstrate the capability of microbe to remediate petroleum hydrocarbon contaminated beach sand. Oil contaminated soil was used as a source of inoculum for hydrocarbon degrading bacteria (HDB) while oil contaminated beach sand was used as remediation object. The growth of HDB in the inocula was enriched and stimulated through the addition of nutrient in the form of vitamin and mineral as well the addition of oil waste as a source of carbon. Experiment took place in the course of approximately five weeks. Microscopic observation clearly showed the interaction between microbe and oil contaminant both in enrichment and bioremediation samples. The result of the experiment also suggests that approximately 25% of the petroleum hydrocarbon mass in the contaminated beach sand was biodegraded over the course of one month. Overall, the results of this experiment suggest the potential of bioremediation method to treat petroleum hydrocarbon polluted environment.Keywords: bacteria, bioremediation, hydrocarbon

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Thormann, Kai M., Renée M. Saville, Soni Shukla, Dale A. Pelletier, and Alfred M. Spormann. "Initial Phases of Biofilm Formation in Shewanella oneidensis MR-1." Journal of Bacteriology 186, no. 23 (December 1, 2004): 8096–104. http://dx.doi.org/10.1128/jb.186.23.8096-8104.2004.

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ABSTRACT Shewanella oneidensis MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism and serves as a model for studying microbially induced dissolution of Fe or Mn oxide minerals as well as biogeochemical cycles. In soil and sediment environments, S. oneidensis biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. In order to develop an understanding of the molecular basis of biofilm formation, we investigated S. oneidensis biofilms developing on glass surfaces in a hydrodynamic flow chamber system. After initial attachment, growth of microcolonies and lateral spreading of biofilm cells on the surface occurred simultaneously within the first 24 h. Once surface coverage was almost complete, biofilm development proceeded with extensive vertical growth, resulting in formation of towering structures giving rise to pronounced three-dimensional architecture. Biofilm development was found to be dependent on the nutrient conditions, suggesting a metabolic control. In global transposon mutagenesis, 173 insertion mutants out of 15,000 mutants screened were identified carrying defects in initial attachment and/or early stages in biofilm formation. Seventy-one of those mutants exhibited a nonswimming phenotype, suggesting a role of swimming motility or motility elements in biofilm formation. Disruption mutations in motility genes (flhB, fliK, and pomA), however, did not affect initial attachment but affected progression of biofilm development into pronounced three-dimensional architecture. In contrast, mutants defective in mannose-sensitive hemagglutinin type IV pilus biosynthesis and in pilus retraction (pilT) showed severe defects in adhesion to abiotic surfaces and biofilm formation, respectively. The results provide a basis for understanding microbe-mineral interactions in natural environments.

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Vu, Minh Thiet, Almando Geraldi, Hoang Dang Khoa Do, Arif Luqman, Hoang Danh Nguyen, Faiza Nur Fauzia, Fahmi Ikhlasul Amalludin, et al. "Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes." Biology 11, no. 5 (April 30, 2022): 695. http://dx.doi.org/10.3390/biology11050695.

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Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.

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Dasgupta, Shamik, Xiaotong Peng, and Kaiwen Ta. "Interaction between Microbes, Minerals, and Fluids in Deep-Sea Hydrothermal Systems." Minerals 11, no. 12 (November 26, 2021): 1324. http://dx.doi.org/10.3390/min11121324.

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The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by converting inorganic carbon into organic biomass. Due to the rich variety of chemical sources and steep physico-chemical gradients, a large array of microorganisms thrive in these extreme environments, which includes but are not restricted to chemolithoautotrophs, heterotrophs, and mixotrophs. Past research has revealed the underlying relationship of these microbial communities with the subsurface geology and hydrothermal geochemistry. Endolithic microbial communities at the ocean floor catalyze a number of redox reactions through various metabolic activities. Hydrothermal chimneys harbor Fe-reducers, sulfur-reducers, sulfide and H2-oxidizers, methanogens, and heterotrophs that continuously interact with the basaltic, carbonate, or ultramafic basement rocks for energy-yielding reactions. Here, we briefly review the global deep-sea hydrothermal systems, microbial diversity, and microbe–mineral interactions therein to obtain in-depth knowledge of the biogeochemistry in such a unique and geologically critical subseafloor environment.

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Zheng, Xingfu, Xuan Pan, Zhenyuan Nie, Yi Yang, Lizhu Liu, Hongying Yang, and Jinlan Xia. "Combined DFT and XPS Investigation of Cysteine Adsorption on the Pyrite (1 0 0) Surface." Minerals 8, no. 9 (August 23, 2018): 366. http://dx.doi.org/10.3390/min8090366.

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The adsorption of cysteine on the pyrite (1 0 0) surface was evaluated by using first-principles-based density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) measurements. The frontier orbitals analyses indicate that the interaction of cysteine and pyrite mainly occurs between HOMO of cysteine and LUMO of pyrite. The adsorption energy calculation shows that the configuration of the -OH of -COOH adsorbed on the Fe site is the thermodynamically preferred adsorption configuration, and it is the strongest ionic bond according to the Mulliken bond populations. As for Fe site mode, the electrons are found transferred from cysteine to Fe of pyrite (1 0 0) surface, while there is little or no electron transfer for S site mode. Projected density of states (PDOS) is analyzed further in order to clarify the interaction mechanism between cysteine and the pyrite (1 0 0) surface. After that, the presence of cysteine adsorption on the pyrite (1 0 0) surface is indicated by the qualitative results of the XPS spectra. This study provides an alternative way to enhance the knowledge of microbe–mineral interactions and find a route to improve the rate of bioleaching.

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Rasmann, Sergio, and Ivan Hiltpold. "Root Exudation of Specialized Molecules for Plant-Environment Interaction." CHIMIA 76, no. 11 (November 30, 2022): 922. http://dx.doi.org/10.2533/chimia.2022.922.

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It has been estimated that between 40 and 60 % of the assimilated carbon is diverted to the roots and released in the rhizosphere in form of root exudates. Root exudates thus define a complex mixture of low and high molecular weight compounds, including carbohydrates, amino acids, organic, and proteins, but also a broad spectrum of specialized molecules, such as flavonoids, glucosinolates, terpenoids, or alkaloids. Root exudates favour soil mineral nutrition, can bind to soil aggregate and in turn modify soil physico-chemical properties, but also mediate plant-plant, plant-microbe, and plant-animal interactions belowground. With this review, we aim to highlight how chemical ecologists have approached the study of root exudates-mediated interactions between plants and their biotic and abiotic surroundings. We do so by presenting a series of study cases for, on one hand, showcasing different methodologies that have been developed to test the activity of different root exudates, and, on the other hand, to show the broad array of interactions mediated by root exudates. Ultimately, we aim to spur further research and collaborations between chemists and ecologists studying belowground chemically-mediated interactions, so as to tackle essential challenges in terms of food security and climate change in the near future.

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Lee, M. R., D. J. Brown, M. E. Hodson, M. Mackenzie, and C. L. Smith. "Weathering microenvironments on feldspar surfaces: implications for understanding fluid-mineral reactions in soils." Mineralogical Magazine 72, no. 6 (December 2008): 1319–28. http://dx.doi.org/10.1180/minmag.2008.072.6.1319.

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AbstractThe mechanisms by which coatings develop on weathered grain surfaces, and their potential impact on rates of fluid-mineral interaction, have been investigated by examining feldspars from a 1.1 ky old soil in the Glen Feshie chronosequence, Scottish highlands. Using the focused ion beam technique, electron-transparent foils for characterization by transmission electron microscopy were cut from selected parts of grain surfaces. Some parts were bare whereas others had accumulations, a few micrometres thick, of weathering products, often mixed with mineral and microbial debris. Feldspar exposed at bare grain surfaces is crystalline throughout and so there is no evidence for the presence of the amorphous ‘leached layers’ that typically form in acid-dissolution experiments and have been described from some natural weathering contexts. The weathering products comprise sub-urn thick crystallites of an Fe-K aluminosilicate, probably smectite, that have grown within an amorphous and probably organic-rich matrix. There is also evidence for crystallization of clays having been mediated by fungal hyphae. Coatings formed within Glen Feshie soils after ∼1.1 ky are insufficiently continuous or impermeable to slow rates of fluid-feldspar reactions, but provide valuable insights into the complex weathering microenvironments on debris and microbe-covered mineral surfaces.

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Ziolkowski, L. A., N. C. S. Mykytczuk, C. R. Omelon, H. Johnson, L. G. Whyte, and G. F. Slater. "Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community." Biogeosciences 10, no. 11 (November 27, 2013): 7661–75. http://dx.doi.org/10.5194/bg-10-7661-2013.

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Abstract. Extreme environmental conditions such as those found in the polar regions on Earth are thought to test the limits of life. Microorganisms living in these environments often seek protection from environmental stresses such as high UV exposure, desiccation and rapid temperature fluctuations, with one protective habitat found within rocks. Such endolithic microbial communities, which often consist of bacteria, fungi, algae and lichens, are small-scale ecosystems comprised of both producers and consumers. However, the harsh environmental conditions experienced by polar endolithic communities are thought to limit microbial diversity and therefore the rate at which they cycle carbon. In this study, we characterized the microbial community diversity, turnover rate and microbe–mineral interactions of a gypsum-based endolithic community in the polar desert of the Canadian high Arctic. 16S/18S/23S rRNA pyrotag sequencing demonstrated the presence of a diverse community of phototrophic and heterotrophic bacteria, archaea, algae and fungi. Stable carbon isotope analysis of the viable microbial membranes, as phospholipid fatty acids and glycolipid fatty acids, confirmed the diversity observed by molecular techniques and indicated that present-day atmospheric carbon is assimilated into the microbial community biomass. Uptake of radiocarbon from atmospheric nuclear weapons testing during the 1960s into microbial lipids was used as a pulse label to determine that the microbial community turns over carbon on the order of 10 yr, equivalent to 4.4 g C m−2 yr−1 gross primary productivity. Scanning electron microscopy (SEM) micrographs indicated that mechanical weathering of gypsum by freeze–thaw cycles leads to increased porosity, which ultimately increases the habitability of the rock. In addition, while bacteria were adhered to these mineral surfaces, chemical analysis by micro-X-ray fluorescence (μ-XRF) spectroscopy suggests little evidence for microbial alteration of minerals, which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe–mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

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Yuliatin, Ervinda. "The Ecological Significance of Plant Growth Promoting Rhizobacteria in Tropical Soil Kalimantan: A Narrative Review." Journal of Tropical Life Science 13, no. 2 (May 25, 2023): 407–20. http://dx.doi.org/10.11594/jtls.13.02.20.

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The diversity of flora in Kalimantan influences the presence of microbe-associated with rhizosphere on their activities and functions in ecosystems. However, abiotic stress such as acidification, drought, and toxic soil residues negatively impacted soil health and plant growth in some regions of Kalimantan's soil. The rhizobacteria, as a group of the plant-growth-promoting rhizobacteria (PGPR), can colonize in the rhizosphere to produce their natural product in making phytohormone for root growth, maintaining soil aggregation and solubilizing the mineral in the soil. Those benefit of rhizobacteria is essential to investigate. However, the study of the role of rhizobacteria in Kalimantan soil interaction with the plant was unclear. Therefore, this review focused on the presence of rhizobacteria and their potency to solve abiotic problems in Kalimantan soil and the underlying mechanism rhizobacteria employs to tolerate harsh soil.

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Dong, H., D. P. Jaisi, J. Kim, and G. Zhang. "Microbe-clay mineral interactions." American Mineralogist 94, no. 11-12 (November 1, 2009): 1505–19. http://dx.doi.org/10.2138/am.2009.3246.

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El-Sawah, Ahmed M., Ali El-Keblawy, Dina Fathi Ismail Ali, Heba M. Ibrahim, Mohamed A. El-Sheikh, Anket Sharma, Yousef Alhaj Hamoud, et al. "Arbuscular Mycorrhizal Fungi and Plant Growth-Promoting Rhizobacteria Enhance Soil Key Enzymes, Plant Growth, Seed Yield, and Qualitative Attributes of Guar." Agriculture 11, no. 3 (February 27, 2021): 194. http://dx.doi.org/10.3390/agriculture11030194.

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Guar is an economically important legume crop that is used for gum production. The clean and sustainable production of guar, especially in newly reclaimed lands, requires biofertilizers that can reduce the use of mineral fertilizers, which have harmful effects on human health and the environment. The present study was conducted to investigate the effects of biofertilizers produced from Bradyrhizobium sp., Bacillus subtilis, and arbuscular mycorrhizal fungi (AMF), individually or in combinations, on microbial activity, and nutrients of the soils and the guar growth and seed quality and yield. The application of biofertilizers improved shoot length, root length, number of branches, plant dry weight, leaf area index (LAI), chlorophyll content, and nutrient uptake of guar plants compared with the control plants. Moreover, the application with biofertilizers resulted in an obvious increase in seed yield and has improved the total proteins, carbohydrates, fats, starch, and guaran contents in the seeds. Additionally, biofertilizer treatments have improved the soil microbial activity by increasing dehydrogenase, phosphatase, protease, and invertase enzymes. Soil inoculation with the optimized doses of biofertilizers saved about 25% of the chemical fertilizers required for the entire guar growth stages. Our results could serve as a practical strategy for further research into integrated plant-microbe interaction in agriculture.

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Ramirez-Villacis, Dario X., Andrea Pinos-Leon, Pamela Vega-Polo, Isai Salas-González, Corbin D. Jones, and Maria de Lourdes Torres. "Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)." Microorganisms 11, no. 2 (February 4, 2023): 399. http://dx.doi.org/10.3390/microorganisms11020399.

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Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant–microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.

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Dong, Hailiang. "Mineral-microbe interactions: a review." Frontiers of Earth Science in China 4, no. 2 (March 27, 2010): 127–47. http://dx.doi.org/10.1007/s11707-010-0022-8.

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Ziolkowski, L. A., N. C. S. Mykytczuk, C. R. Omelon, H. Johnson, L. G. Whyte, and G. F. Slater. "Arctic Gypsum Endoliths: a biogeochemical characterization of a viable and active microbial community." Biogeosciences Discussions 10, no. 2 (February 8, 2013): 2269–304. http://dx.doi.org/10.5194/bgd-10-2269-2013.

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Abstract. Extreme environmental conditions such as those found in the polar regions on Earth are thought to test the limits of life. Microorganisms living in these environments often seek protection from environmental stresses such as high UV exposure, desiccation and rapid temperature fluctuations, with one protective habitat found within rocks. Such endolithic microbial communities, which often consist of bacteria, fungi, algae and lichens, are small-scale ecosystems comprised of both producers and consumers. However, the harsh environmental conditions experienced by polar endolithic communities are thought to limit microbial diversity and the rate at which they cycle carbon. In this study, we characterized the microbial community diversity, turnover, and microbe-mineral interactions of a gypsum-based endolithic community in the polar desert of the Canadian high Arctic. 16S/18S rRNA pyrotag sequencing demonstrated the presence of a diverse community of phototrophic and heterotrophic bacteria, algae and fungi. Stable carbon isotope analysis of the viable microbial membranes, as phospholipid fatty acids and glycolipid fatty acids, confirmed the diversity observed by molecular techniques and indicated that atmospheric carbon is assimilated into the microbial community biomass. Uptake of radiocarbon from atmospheric radioweapons testing during the 1960s into microbial lipids was used as a pulse label to determine that the microbial community turns over carbon on the order of 10 yr, equivalent to 4.4 g C m−2 yr−1 gross primary productivity. SEM micrographs indicated that mechanical weathering of gypsum by freeze-thaw cycles leads to increased porosity, which ultimately increases the habitability of the rock. In addition, while bacteria were adhered to these mineral surfaces there was little evidence for microbial alteration of minerals, which contrasts with other gypsum endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbial-mineral interaction, an alternative hypothesis is that the soluble and friable nature of the gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

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Johnston, Vanessa, Andrea Martín-Pérez, Sara Skok, and Janez Mulec. "Microbially-mediated carbonate dissolution and precipitation; towards a protocol for ex-situ, cave-analogue cultivation experiments." International Journal of Speleology 50, no. 2 (April 2021): 137–55. http://dx.doi.org/10.5038/1827-806x.50.2.2372.

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Subterranean calcite dissolution and precipitation are often considered as strictly geochemical processes. The active involvement of microbes in these processes is commonly underestimated in the literature due to general oligotrophic conditions in caves, except in particular cave conditions, such as sulfidic caves and moonmilk deposits, where the presence of microbes likely plays a key role in mineral deposition. Here, we study the possible involvement of microbes from Postojna Cave, Slovenia, in carbonate dissolution (litholysis) and precipitation (lithogenesis). Microbes were sampled from small pools below hydrologically diverse drip sites and incubated on polished limestone tablets at 10 and 20°C for 2 and 14 weeks under cave-analogue conditions. The tablets were then observed under scanning electron microscope to investigate microbe–rock interactions. Our experiments showed the presence of various microbial morphotypes, often associated with extracellular polymeric substances, firmly attached on the surfaces. Unfortunately, our surface sterilization method using 96% and 70% ethanol could not establish the complete aseptic conditions in deep natural cracks in the experimental limestone tablets. Nonetheless, our results emulate the interaction of environmental microbes with limestone rock. Conspicuous calcite dissolution and precipitation were observed in association with these microbes. Furthermore, we show evidence of entombment of microbes in a Si-rich precipitate during nutrient-depleted growth conditions and we suggest that microbial involvement in silica mobilization under ambient conditions may be a widespread and often overlooked phenomenon. Our findings have important implications for microbial-mediation of cave carbonate dissolution and precipitation, including the preservation of past climate proxy signals in speleothems and prehistoric cave art. Improvements to the methodology and further work are suggested to enable more robust ex-situ cultivation experiments in the future, facilitating better and more detailed research into this topic.

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Asadi, Mohammad, Farzad Rasouli, Trifa Amini, Mohammad Bagher Hassanpouraghdam, Somaye Souri, Sona Skrovankova, Jiri Mlcek, and Sezai Ercisli. "Improvement of Photosynthetic Pigment Characteristics, Mineral Content, and Antioxidant Activity of Lettuce (Lactuca sativa L.) by Arbuscular Mycorrhizal Fungus and Seaweed Extract Foliar Application." Agronomy 12, no. 8 (August 18, 2022): 1943. http://dx.doi.org/10.3390/agronomy12081943.

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Beneficial plant–microbe interaction for enhancing crop yield and quality is a sustainable way to achieve eco-friendly, desirable agricultural productions. The main objective of this experiment was to evaluate the individual and combined effects of an arbuscular mycorrhizal fungus (AMF) strain (Funneliformis mosseae) and a seaweed extract (SWE) derived from Ascophyllum nodosum, on the growth and physiological responses of lettuce (Lactuca sativa L.). Lettuce plants were inoculated with commercial AMF inoculum (5 g kg−1 soil), and SWE foliar application was done at three levels (0.5, 1.5, and 3 g L−1). The findings revealed that AMF along with SWE generated the greatest impact. In fact, co-application of AMF inoculation and 3 g L−1 SWE considerably enhanced root colonization, chlorophyll a, chlorophyll b, total chlorophyll, carotenoids, and mineral content in the shoots and roots (N, P, K, Ca, Fe, Zn, and Mn content) of lettuce plants. This combination improved initial fluorescence (F0), photochemical efficiency of PSII (FV/Fm) and Y(NO) and total antioxidant activity (TAA), whereas the maximum fluorescence, (Fm) and Y(II), showed the highest increase in lettuce plants treated with AMF and 1.5 g L−1 SWE. Furthermore, AMF inoculation along with SWE, at concentrations 1.5 and 3 g L−1, considerably enhanced variable fluorescence (FV) and the activity of water decomposition in electron donor photosystem II (FV/F0). As a result of these findings, it can be stated that the co-application of AMF and SWE positively improves the growth and development of lettuce plants.

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Nie, Zhen Yuan, Hong Chang Liu, Jin Lan Xia, Huan Liu, Yun Lu Cui, and Guan Zhou Qiu. "Evolution of Compositions and Contents of Capsule and Slime EPSs for Adaptation to and Action on Energy Substrates and Heavy Metals by Typical Bioleaching Microorganisms." Solid State Phenomena 262 (August 2017): 466–70. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.466.

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Adaption to the energy substrates and heavy metals by bioleaching micoorganisms is the prerequisite for efficient microbe-mineral interaction in bioleaching process. It is known extracellular polymer substances (EPSs) take important role in mediating the adaption to and action on energy substrates and heavy metals. This report presents the evolution of compositions and contents of the major components of EPSs of the typical bioleaching microorganisms (Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Acidianus manzaensis,) exposed to different energy substrates and heavy metal ions. These strains were acclimated firstly to Fe2+ substrate, and then on the substrates elemental sulfur (S0), pyrite and chalcopyrite, respectively. It was found that the major components of capsule and slime EPSs in terms of proteins, polysaccharides, as well as uronic acids were quite different in contents for the Fe2+-acclimated strains, and they even changed more when the Fe2+-acclimated strains were further acclimated to the other substrates. When exposed to heavy metals, all strains demonstrated much decrease in contents of capsule EPSs, and much increase in slime EPSs contents and the heavy metals were found to bound to the slime parts. It was for the first time the EPSs of the bioleaching strains were fractionated into capsule part and slime part, and it was also for the first time we found the differences in evolution of compositions and contents of the major organic components as well as the inorganic matter of capsule EPSs and slime EPSs when the bioleaching strains were exposed to different energy substrates and heavy metals.

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Dong, Hailiang, and Anhuai Lu. "Geomicrobiology Research in China: Mineral-Microbe Interactions." Geomicrobiology Journal 29, no. 3 (April 2012): 197–98. http://dx.doi.org/10.1080/01490451.2012.640602.

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Dong, Hailiang. "Electron Microscopic Characterization of Mineral-Microbe Interactions." Microscopy and Microanalysis 25, S2 (August 2019): 2350–51. http://dx.doi.org/10.1017/s1431927619012480.

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Mapelli, Francesca, Ramona Marasco, Annalisa Balloi, Eleonora Rolli, Francesca Cappitelli, Daniele Daffonchio, and Sara Borin. "Mineral–microbe interactions: Biotechnological potential of bioweathering." Journal of Biotechnology 157, no. 4 (February 2012): 473–81. http://dx.doi.org/10.1016/j.jbiotec.2011.11.013.

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Gates, Will P. "Methods for Study of Microbe-Mineral Interactions." Clays and Clay Minerals 56, no. 1 (February 2008): 128–29. http://dx.doi.org/10.1007/bf03406036.

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Dong, H., and A. Lu. "Mineral-Microbe Interactions and Implications for Remediation." Elements 8, no. 2 (April 1, 2012): 95–100. http://dx.doi.org/10.2113/gselements.8.2.95.

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Saunders, Scott H., and Dianne K. Newman. "Extracellular Electron Transfer Transcends Microbe-Mineral Interactions." Cell Host & Microbe 24, no. 5 (November 2018): 611–13. http://dx.doi.org/10.1016/j.chom.2018.10.018.

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Hudson-Edwards, Karen, and Joanne Santini. "Arsenic-Microbe-Mineral Interactions in Mining-Affected Environments." Minerals 3, no. 4 (October 9, 2013): 337–51. http://dx.doi.org/10.3390/min3040337.

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HU, R., S. LI, F. LI, M. YANG, Z. JIN, X. LI, and F. ZHANG. "MINERAL-MICROBE INTERACTIONS: BACTERIALLY INDUCED HYDRATION OF BIOTITE." Applied Ecology and Environmental Research 19, no. 3 (2021): 2037–47. http://dx.doi.org/10.15666/aeer/1903_20372047.

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Siradje, Andi Lindhemuthianingrum, Irfan D. Prijambada, and Endah Retnaningrum. "Biofilm Formation of Pseudomonas geniculata (Wright, 1895) Chester, 1901 on Three Fungals Species: Relationship with Incubation Time and Fungal Diameter Size." KnE Life Sciences 3, no. 4 (March 27, 2017): 28. http://dx.doi.org/10.18502/kls.v3i4.684.

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Pseudomonas geniculata has been isolated from uncontaminated vertisol in Kulon Progo district. The isolate is hydrocarbonoclastic bacterium capable of forming biofilm on the fungal hyphae. Sinergy of both microbe in the form fungal-bacteria biofilm produce high ability to degrading hydrocarbon and survive in its pollution environment. The purpose of this research was to evaluate ability of Pseudomonas geniculata (Wright, 1895) Chester, 1901 to form biofilm and its attachment on three fungals species such as Penicillium sp., Penicillium funiculosum and Penicillium crustosum. The diameter size of fungal hyphae was of 1.3 µm, 1.9 µm and 2.4 µm, respectively. P. geniculata required at least 48 h to form biofilms on Penicillium sp. hyphae when incubated in mineral Bushnell Haas Medium suplemented with 2 % glucose at room temperature, with maximal biofilm formation being evident at 360 h. Biofilm attachment on Penicillium sp. hyphae was disrupted by the vortex power of 5 rpm for 20 s. Interaction of P. geniculata and Penicillium sp. that has a smallest diameter size of hypha were more successful on biofilm formation and attachment which could contribute to bacterial survival in environmental stresses. <div>Keyword: Biofilm, fungal hyphae, Pseudomonas geniculata (Wright, 1895) Chester, 1901, Penicillium. </div>

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Scott, Jill R., Beizhan Yan, and Daphne L. Stoner. "Spatially-correlated mass spectrometric analysis of microbe–mineral interactions." Journal of Microbiological Methods 67, no. 2 (November 2006): 381–84. http://dx.doi.org/10.1016/j.mimet.2006.04.020.

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Kemner, K. M., E. J. O'Loughlin, S. D. Kelly, and M. I. Boyanov. "Synchrotron X-ray Investigations of Mineral-Microbe-Metal Interactions." Elements 1, no. 4 (September 1, 2005): 217–21. http://dx.doi.org/10.2113/gselements.1.4.217.

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Mishra, Bhoopesh. "Towards a mechanistic understanding of mercury–microbe/mineral interactions." Acta Crystallographica Section A Foundations and Advances 73, a2 (December 1, 2017): C333. http://dx.doi.org/10.1107/s2053273317092403.

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Brown, G. E., Y. Wang, A. Gélabert, J. Ha, C. Cismasu, G. Ona-Nguema, K. Benzerara, et al. "Synchrotron X-ray studies of heavy metal mineral-microbe interactions." Mineralogical Magazine 72, no. 1 (February 2008): 169–73. http://dx.doi.org/10.1180/minmag.2008.072.1.169.

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The availability of analytical methods that utilize the very intense and bright X-rays from synchrotron radiation sources has fundamentally changed the way in which geoscientists, environmental scientists and soil scientists study complex environmental samples and decipher the chemical and biological processes that impact the speciation, transport and potential bioavailability of environmental toxins (Brown et al., 2006). Such samples are often mixtures of crystalline and amorphous phases in particle-sizes ranging from cm to nm, adsorbed metal ions and organic molecules, natural organic matter, microbial organisms, algae, plant materials and aqueous solutions. The processes that affect the chemical forms and environmental fate of contaminants in such mixtures range from surface adsorption, desorption, precipitation and dissolution reactions, often involving a combination of hydrolysis, ligand exchange and electron transfer, to biological interactions in which microbial organisms, algae or plants interact with mineral surfaces and environmental contaminants.

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Pett-Ridge, Jennifer, and Mary K. Firestone. "Using stable isotopes to explore root-microbe-mineral interactions in soil." Rhizosphere 3 (June 2017): 244–53. http://dx.doi.org/10.1016/j.rhisph.2017.04.016.

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Cockell, Charles S. "Geomicrobiology beyond Earth: microbe–mineral interactions in space exploration and settlement." Trends in Microbiology 18, no. 7 (July 2010): 308–14. http://dx.doi.org/10.1016/j.tim.2010.03.005.

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Cockell, Charles S. "Synthetic geomicrobiology: engineering microbe–mineral interactions for space exploration and settlement." International Journal of Astrobiology 10, no. 4 (May 27, 2011): 315–24. http://dx.doi.org/10.1017/s1473550411000164.

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AbstractSynthetic geomicrobiology is a potentially new branch of synthetic biology that seeks to achieve improvements in microbe–mineral interactions for practical applications. In this paper, laboratory and field data are provided on three geomicrobiology challenges in space: (1) soil formation from extraterrestrial regolith by biological rock weathering and/or the use of regolith as life support system feedstock, (2) biological extraction of economically important elements from rocks (biomining) and (3) biological solidification of surfaces and dust control on other planetary surfaces. The use of synthetic or engineered organisms in these three applications is discussed. These three examples are used to extract general common principles that might be applied to the design of organisms used in synthetic geomicrobiology.

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Edwards, Katrina J., Wolfgang Bach, and Thomas M. McCollom. "Geomicrobiology in oceanography: microbe–mineral interactions at and below the seafloor." Trends in Microbiology 13, no. 9 (September 2005): 449–56. http://dx.doi.org/10.1016/j.tim.2005.07.005.

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Vaughan, David J., and Jonathan R. Lloyd. "Mineral-organic-microbe interactions: Environmental impacts from molecular to macroscopic scales." Comptes Rendus Geoscience 343, no. 2-3 (February 2011): 140–59. http://dx.doi.org/10.1016/j.crte.2010.10.005.

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Loudon, Claire-Marie, Natasha Nicholson, Kai Finster, Natalie Leys, Bo Byloos, Rob Van Houdt, Petra Rettberg, et al. "BioRock: new experiments and hardware to investigate microbe–mineral interactions in space." International Journal of Astrobiology 17, no. 4 (July 24, 2017): 303–13. http://dx.doi.org/10.1017/s1473550417000234.

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AbstractIn this paper, we describe the development of an International Space Station experiment, BioRock. The purpose of this experiment is to investigate biofilm formation and microbe–mineral interactions in space. The latter research has application in areas as diverse as regolith amelioration and extraterrestrial mining. We describe the design of a prototype biomining reactor for use in space experimentation and investigations onin situResource Use and we describe the results of pre-flight tests.

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Ahmed, Engy, and Sara J. M. Holmström. "Microbe–mineral interactions: The impact of surface attachment on mineral weathering and element selectivity by microorganisms." Chemical Geology 403 (May 2015): 13–23. http://dx.doi.org/10.1016/j.chemgeo.2015.03.009.

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DAVIS, K. J., K. H. NEALSON, and A. LÜTTGE. "Calcite and dolomite dissolution rates in the context of microbe?mineral surface interactions." Geobiology 5, no. 2 (June 2007): 191–205. http://dx.doi.org/10.1111/j.1472-4669.2007.00112.x.

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Journal articles on the topic 'Microbe-mineral Interaction'

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