Geomicrobiology: How Molecular-Scale Interactions Underpin Biogeochemical Systems

  title={Geomicrobiology: How Molecular-Scale Interactions Underpin Biogeochemical Systems},
  author={Dianne K. Newman and Jillian F. Banfield},
  pages={1071 - 1077}
Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities… 

Functional metagenomic profiling of nine biomes

The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.


In the last few years, the wealth of new information on microbial diversity, metabolic capabilities, and environmental constraints has led to significant insights into the ways in which microbes


Future work will further pursue these avenues, with frequent use of modern, molecular methods to ascertain the role of individual species and species diversity in ecosystem function.

The genetics of geochemistry.

Bacterial genetics holds the key to understanding when and to what extent these metabolisms influence modern geochemical cycles, as well as develop a basis for deciphering their origins and how organisms that utilized them may have altered the chemical and physical features of the authors' planet.

Scaling up: the next challenge in environmental microbiology.

Concept and technical challenges for some key microbially mediated environmental processes, problems and extremes that require synthesizing growing knowledge of microbial community structure with emerging knowledge of function in aquatic ecosystems are discussed.

Endolithic microbial ecosystems.

Comparison of endolithic communities supports the principle that patterns of microbial diversity are governed by similar principles observed in macroecological systems.

The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses.

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites.

6.5 Biospeleogenesis




Merging Genomes with Geochemistry in Hydrothermal Ecosystems

Clues to the strategies for how life thrives in dynamic ecosystems are beginning to be elucidated through a confluence of biogeochemistry, microbiology, ecology, molecular biology, and genomics, which could reveal how ecosystems originate, the extent of the subsurface biosphere, and the driving forces of evolution.

A molecular view of microbial diversity and the biosphere.

Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial,

Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis

These results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms and indicate assimilation of isotopically light methane into specific archaeal cells.

Microbial Activity at Gigapascal Pressures

Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system.

A Chemoautotrophically Based Cave Ecosystem

Analysis of stable carbon and nitrogen isotopes showed that this chemoautotrophic production is the food base for 48 species of cave-adapted terrestrial and aquatic invertebrates, 33 of which are endemic to this ecosystem.

Microbial Life in the Underworld: Biogenicity in Secondary Mineral Formations

One unresolved issue in geomicrobiology is the involvement of microbial activity in the formation of secondary mineral deposits, or speleothems, in caves. Although there is extensive literature

A hydrogen-based subsurface microbial community dominated by methanogens

This work describes a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria and demonstrates that hydrogen-based methanogenic communities do occur in Earth's subsurfaces, providing an analogue for possible subsurfaced microbial ecosystems on other planets.

Diversity of Sulfate-Reducing Bacteria in Oxic and Anoxic Regions of a Microbial Mat Characterized by Comparative Analysis of Dissimilatory Sulfite Reductase Genes

The most highly diverse DSR sequences, most related to those of the Desulfonema-like organisms within the δ-proteobacteria, were recovered from oxic regions of the mat, extending those of previous studies by us and others associating Desulf onema- like organisms with oxic habitats.

Dense populations of a giant sulfur bacterium in Namibian shelf sediments.

A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system, and is closely related to the marine filamentous sulfur bacteria Thioploca, abundant in the up welling area off Chile and Peru.

Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes

Direct evidence supporting the coexistence and distribution of multiple ecotypes permits the survival of the population as a whole over a broader range of environmental conditions than would be possible for a homogeneous population is reported.