Understanding Microbially Active Biogeochemical Environments

Isolation and characterization of mineral-dissolving bacteria from different levels of altered mica schist surfaces and the adjacent soil

Microorganisms play important role in mineral weathering. However, little is known about rock-associated mineral-dissolving bacteria. In this study, 129 bacterial isolates were obtained from the less and more weathered mica schist surfaces and the adjacent soil and characterized for mineral dissolving activity, population, and the linkage of rock weathering level and distribution of the bacteria. Among the 129 isolates, 112 isolates could dissolve biotite. The relative abundance of the highly effective Fe solubilizers was significantly higher on the more altered rock surface (89.6%) than in the soil (51.2%) and on the less altered rock surface (22.5%), while the relative abundance of the highly effective Si solubilizers was significantly higher in the soil (65.9%) than on the more (41.7%) and less (12.5%) altered rock surfaces. Furthermore, 17.5-42.5%, 87.5%, and 60.9-90.2% of the highly effective acid- and siderophore-producing isolates were obtained in the less and more weathered rocks and the soil, respectively. The mineral-dissolving bacteria belonged to 18 genera and Burkholderia, Bacillus, and Paenibacillus were the dominant and highly effective mineral-dissolving bacteria. Phylogenetic analysis found 2, 9, and 5 bacterial species in the highly effective mineral-dissolving bacteria on the less and more altered rock surfaces and in the soil, respectively. The results showed the abundant and diverse mineral-dissolving bacterial populations on the more weathered rock surfaces. The results also suggested distinct mineral-dissolving activities and mechanisms of the bacteria and highlighted the possibility for the development of bacterial inocula for plant nutrition improvement in silicate mineral-rich soils.

Differences in weathering pattern, stress resistance and community structure of culturable rock-weathering bacteria between altered rocks and soils

In this study, we isolated and characterized rock-weathering bacteria from the surfaces of less and more altered tuffs, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in these rocks and soils. Using a moderate-nutrition medium, we obtained 150 isolates from the rocks and soils. The rock-weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, and Fe released from tuff under aerobic conditions. Based on the potential of the bacterial influence on the element releases, the isolates could be grouped into highly, moderately, and least effective element solubilizers, respectively. Significantly more highly effective Al and Fe solubilizers were observed in the altered rocks, while the soils had more highly effective Si solubilizers. Furthermore, more isolates from the altered rocks significantly acidified the culture medium in the rock weathering process. Dynamic changes in the element release showed the distinct element releasing patterns of three selected isolates. More isolates from the altered rocks could grow at 4 °C or at 55 °C or at pH 4. Some isolates from the altered rocks could grow at pH 10 and with 10–15% (w/v) NaCl. The altered rocks and the soils existed in diverse and different highly weathering-specific culturable rock-weathering community structures. The changes in the culturable weathering communities between the altered rocks and the soils were attributable not only to major bacterial groups but also to a change in the minor population structure.

Rock-weathering bacteria from the surfaces of less and more altered tuffs were isolated and characterized, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in the rocks and soils.

Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain

Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10⁶-10⁷ colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH < 4.0) in the rock dissolution process. Most rock-weathering bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.

Geomycology: metals, actinides and biominerals

Geomycology can be simply defined as 'the scientific study of the roles of fungi in processes of fundamental importance to geology' and the biogeochemical importance of fungi is significant in several key areas. These include nutrient and element cycling, rock and mineral transformations, bioweathering, mycogenic biomineral formation and interactions of fungi with clay minerals and metals. Such processes can occur in aquatic and terrestrial habitats, but it is in the terrestrial environment where fungi probably have the greatest geochemical influence. Of special significance are the mutualistic relationships with phototrophic organisms, lichens (algae, cyanobacteria) and mycorrhizas (plants). Central to many geomycological processes are transformations of metals and minerals, and fungi possess a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Some fungal transformations have beneficial applications in environmental biotechnology, e.g. in metal and radionuclide leaching, recovery, detoxification and bioremediation, and in the production or deposition of biominerals or metallic elements with catalytic or other properties. Metal and mineral transformations may also result in adverse effects when these processes result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment. The ubiquity and importance of fungi in biosphere processes underlines the importance of geomycology as an interdisciplinary subject area within microbiology and mycology.

Microbial community diversity of moonmilk deposits at Ballynamintra Cave, Co. Waterford, Ireland

Caves are extreme and specialised habitats for terrestrial life that sometimes contain moonmilk, a fine-grained paste-like secondary mineral deposit that is found in subterranean systems worldwide. While previous studies have investigated the possible role of microorganisms in moonmilk precipitation, the microbial community ecology of moonmilk deposits is poorly understood. Bacterial and fungal community structure associated with four spatially isolated microcrystalline, acicular calcite moonmilk deposits at Ballynamintra Cave (S. Ireland) was investigated during this study. Statistical analyses revealed significant differences in microbial activity, number of bacterial species, bacterial richness and diversity, and fungal diversity (Shannon's diversity) among the moonmilk sites over an area of approximately 2.5 m(2). However, the number of fungal species and fungal community richness were unaffected by sampling location. SIMPER analysis revealed significant differences in bacterial and fungal community composition among the sampling sites. These data suggest that a rich assemblage of microorganisms exists associated with moonmilk, with some spatial diversity, which may reflect small-scale spatial differences in cave biogeochemistry.

Metals, minerals and microbes: geomicrobiology and bioremediation

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.