Geomicrobiology is the scientific field at the intersection of geology and microbiology and is a major subfield of geobiology. It concerns the role of microbes on geological and geochemical processes and effects of minerals and metals to microbial growth, activity and survival. Such interactions occur in the geosphere, the atmosphere and the hydrosphere. Geomicrobiology studies microorganisms that are driving the Earth's biogeochemical cycles, mediating mineral precipitation and dissolution, and sorbing and concentrating metals. The applications include for example bioremediation, mining, climate change mitigation and public drinking water supplies.
Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.
Geobacter is a genus of bacteria. Geobacter species are anaerobic respiration bacterial species which have capabilities that make them useful in bioremediation. Geobacter was found to be the first organism with the ability to oxidize organic compounds and metals, including iron, radioactive metals, and petroleum compounds into environmentally benign carbon dioxide while using iron oxide or other available metals as electron acceptors. Geobacter species are also found to be able to respire upon a graphite electrode. They have been found in anaerobic conditions in soils and aquatic sediment.
In biology, syntrophy, synthrophy, or cross-feeding is the phenomenon of one species feeding on the metabolic products of another species to cope up with the energy limitations by electron transfer. In this type of biological interaction, metabolite transfer happens between two or more metabolically diverse microbial species that live in close proximity to each other. The growth of one partner depends on the nutrients, growth factors, or substrates provided by the other partner. Thus, syntrophism can be considered as an obligatory interdependency and a mutualistic metabolism between two different bacterial species.
A brine pool, sometimes called an underwater lake, deepwater or brine lake, is a volume of brine collected in a seafloor depression. The pools are dense bodies of water that have a salinity that is three to eight times greater than the surrounding ocean. Brine pools are commonly found below polar sea ice and in the deep ocean. Those below sea ice form through a process called brine rejection. For deep-sea brine pools, salt is necessary to increase the salinity gradient. The salt can come from one of two processes: the dissolution of large salt deposits through salt tectonics or geothermally heated brine issued from tectonic spreading centers.
Nitrospira translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems, natural biological marine settings, water circulation biofilters in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii. In addition, Nitrospira bacteria's 16s rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete nitrification has also been discovered and cultivated.
Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota. It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically important groups of bacteria belong to this class. It is composed by all Gram-negative microbes and is the most phylogenetically and physiologically diverse class of Proteobacteria.
The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Saccharibacteria, formerly known as TM7, is a major bacterial lineage. It was discovered through 16S rRNA sequencing.
The class Zetaproteobacteria is the sixth and most recently described class of the Pseudomonadota. Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria were originally represented by a single described species, Mariprofundus ferrooxydans, which is an iron-oxidizing neutrophilic chemolithoautotroph originally isolated from Kamaʻehuakanaloa Seamount in 1996 (post-eruption). Molecular cloning techniques focusing on the small subunit ribosomal RNA gene have also been used to identify a more diverse majority of the Zetaproteobacteria that have as yet been unculturable.
"Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetales. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.
Hadesarchaea, formerly called the South-African Gold Mine Miscellaneous Euryarchaeal Group, are a class of thermophile microorganisms that have been found in deep mines, hot springs, marine sediments, and other subterranean environments.
"Candidatus Thorarchaeota", or simply Thorarchaeota, is a phylum within the superphylum Asgard archaea. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes. Since there is such a close relation between the two different domains, it provides further evidence to the two-domain tree of life theory which states that eukaryotes branched from the archaeal domain. Asgard archaea are single cell marine microbes that contain branch like appendages and have genes that are similar to eukarya. The asgard archaea superphylum is composed of Thorarchaeota, Lokiarchaeota, Odinarchaeota, and Heimdallarchaeota. Thorarchaeota were first identified from the sulfate-methane transition zone in tidewater sediments. Thorarcheota are widely distributed in marine and freshwater sediments.
The deep biosphere is the part of the biosphere that resides below the first few meters of the surface. It extends down at least 5 kilometers below the continental surface and 10.5 kilometers below the sea surface, at temperatures that may reach beyond 120 °C, which is comparable to the maximum temperature where a metabolically active organism has been found. It includes all three domains of life and the genetic diversity rivals that on the surface.
Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.
Fermentibacteria is a bacterial phylum with candidate status. It is part of the FCB group.
Berkelbacteria is a bacterial phylum with candidate status, meaning there are no cultured representatives for this group. It is part of the Candidate Phyla Radiation.
Modulibacteria is a bacterial phylum formerly known as KS3B3 or GN06. It is a candidate phylum, meaning there are no cultured representatives of this group. Members of the Modulibacteria phylum are known to cause fatal filament overgrowth (bulking) in high-rate industrial anaerobic wastewater treatment bioreactors.
NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.
