ALBERT

Description: © The Author(s), 2014]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 6648, doi:10.1038/srep06648.

Description: Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

Description: This research was supported by grants from the National Natural Science Foundation of China (Grant Nos. 41030211 and 41302022), the National Basic Research Program of China (Grant No. 2011CB808800), and State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Nos GBL11410 and GBL11201).

Description: Electron energy-loss spectroscopy (EELS), energy-filtered transmission electron microscopy (EFTEM), and high-resolution transmission electron microscopy (HRTEM) have been applied in mineralogy and materials research to determine the oxidation states of various metals at high spatial resolution. Such information is critical in understanding the kinetics and mechanisms of mineral-microbe interactions. To date, the aforementioned techniques have not been applied widely in the study of such interactions. In the present study, the three techniques above were employed to investigate mineral transformations associated with microbial Fe(III) reduction in magnetite. Shewanella putrefaciens strain CN32, a dissimilatory metal-reducing bacterium, was incubated with magnetite as the sole electron acceptor and lactate as the electron donor for 14 days under anoxic conditions in bicarbonate buffer. The extent of bioreduction was determined by wet chemistry and mineral solids were investigated by HRTEM, EFTEM, and EELS. Magnetite was partially reduced and biogenic siderite formed. The elemental maps of Fe, O, and C and red-green-blue (RGB) composite map for residual magnetite and newly formed siderite were contrasted by the EFTEM technique. The HRTEM revealed nm-sized magnetite crystals coating bacterial cells. The Fe oxidation state in residual magnetite and biogenic siderite was determined using the EELS technique (the integral ratio of L3 to L2). The integral ratio of L3 to L2 for magnetite (6.29) and siderite (2.71) corresponded to 71% of Fe(III) in magnetite, and 24% of Fe(III) in siderite, respectively. A chemical shift (~1.9 eV) in the Fe-L3 edge of magnetite and siderite indicated a difference in the oxidation state of Fe between these two minerals. Furthermore, the EELS images of magnetite (709 eV) and siderite (707 eV) were extracted from the electron energy-loss spectra collected, ranging from 675 to 755 eV, displaying different oxidation states of Fe in the magnetite and siderite phases. The results demonstrate that EELS is a powerful technique for studying the Fe oxidation-state change as a result of microbial interaction with Fe-containing minerals.

Description: Minerals and microbes have coevolved throughout much of Earth history. They interact at the microscopic scale, but their effects are manifested macroscopically. Minerals support microbial growth by providing essential nutrients, and microbial activity alters mineral solubility and the oxidation state of certain constituent elements. Microbially mediated dissolution, precipitation, and transformation of minerals are either directly controlled by microorganisms or induced by biochemical reactions that usually take place outside the cell. All these reactions alter metal mobility, leading to the release or sequestration of heavy metals and radionuclides. These processes therefore have implications for ore formation and the bioremediation of contaminated sites.

Description: Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks, and they play important roles in environmental processes. Microbes are also abundant in these geological media, and they interact with clays via a variety of mechanisms, such as reduction and oxidation of structural iron and mineral dissolution and precipitation through the production of siderophores and organic acids. These interactions greatly accelerate clay mineral reaction rates. While it is certain that microbes play important roles in clay mineral transformations, quantitative assessment of these roles is limited. This paper reviews some active areas of research on clay–microbe interactions and provides perspectives for future work.

Description: The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic (Shewanella putrefaciens CN32) and thermophilic (Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65{degrees}C) were the most favorable conditions for the formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

Description: Electron energy-loss spectroscopy (EELS), energy-filtered transmission electron microscopy (EFTEM), and high-resolution transmission electron microscopy (HRTEM) have been applied in mineralogy and materials research to determine the oxidation states of various metals at high spatial resolution. Such information is critical in understanding the kinetics and mechanisms of mineral-microbe interactions. To date, the aforementioned techniques have not been applied widely in the study of such interactions. In the present study, the three techniques above were employed to investigate mineral transformations associated with microbial Fe(III) reduction in magnetite. Shewanella putrefaciens strain CN32, a dissimilatory metal-reducing bacterium, was incubated with magnetite as the sole electron acceptor and lactate as the electron donor for 14 days under anoxic conditions in bicarbonate buffer. The extent of bioreduction was determined by wet chemistry and mineral solids were investigated by HRTEM, EFTEM, and EELS. Magnetite was partially reduced and biogenic siderite formed. The elemental maps of Fe, O, and C and red-green-blue (RGB) composite map for residual magnetite and newly formed siderite were contrasted by the EFTEM technique. The HRTEM revealed nm-sized magnetite crystals coating bacterial cells. The Fe oxidation state in residual magnetite and biogenic siderite was determined using the EELS technique (the integral ratio of L3 to L2). The integral ratio of L3 to L2 for magnetite (6.29) and siderite (2.71) corresponded to 71% of Fe(III) in magnetite, and 24% of Fe(III) in siderite, respectively. A chemical shift (~1.9 eV) in the Fe-L3 edge of magnetite and siderite indicated a difference in the oxidation state of Fe between these two minerals. Furthermore, the EELS images of magnetite (709 eV) and siderite (707 eV) were extracted from the electron energy-loss spectra collected, ranging from 675 to 755 eV, displaying different oxidation states of Fe in the magnetite and siderite phases. The results demonstrate that EELS is a powerful technique for studying the Fe oxidation-state change as a result of microbial interaction with Fe-containing minerals.

Description: Electron energy-loss spectroscopy (EELS), energy-filtered transmission electron microscopy (EFTEM), and high-resolution transmission electron microscopy (HRTEM) have been applied in mineralogy and materials research to determine the oxidation states of various metals at high spatial resolution. Such information is critical in understanding the kinetics and mechanisms of mineral-microbe interactions. To date, the aforementioned techniques have not been applied widely in the study of such interactions. In the present study, the three techniques above were employed to investigate mineral transformations associated with microbial Fe(III) reduction in magnetite. Shewanella putrefaciens strain CN32, a dissimilatory metal-reducing bacterium, was incubated with magnetite as the sole electron acceptor and lactate as the electron donor for 14 days under anoxic conditions in bicarbonate buffer. The extent of bioreduction was determined by wet chemistry and mineral solids were investigated by HRTEM, EFTEM, and EELS. Magnetite was partially reduced and biogenic siderite formed. The elemental maps of Fe, O, and C and red-green-blue (RGB) composite map for residual magnetite and newly formed siderite were contrasted by the EFTEM technique. The HRTEM revealed nm-sized magnetite crystals coating bacterial cells. The Fe oxidation state in residual magnetite and biogenic siderite was determined using the EELS technique (the integral ratio of L3 to L2). The integral ratio of L3 to L2 for magnetite (6.29) and siderite (2.71) corresponded to 71% of Fe(III) in magnetite, and 24% of Fe(III) in siderite, respectively. A chemical shift (~1.9 eV) in the Fe-L3 edge of magnetite and siderite indicated a difference in the oxidation state of Fe between these two minerals. Furthermore, the EELS images of magnetite (709 eV) and siderite (707 eV) were extracted from the electron energy-loss spectra collected, ranging from 675 to 755 eV, displaying different oxidation states of Fe in the magnetite and siderite phases. The results demonstrate that EELS is a powerful technique for studying the Fe oxidation-state change as a result of microbial interaction with Fe-containing minerals.