Inside the Atacama Desert: uncovering the living microbiome of an extreme environment.

The Atacama Desert in Chile is one of the driest and most inhospitable places on Earth. To analyze the diversity and distribution of microbial communities in such an environment, one of the most important and challenging steps is DNA extraction. Using commercial environmental DNA extraction protocols, a mixture of living, dormant, and dead cells of microorganisms is extracted, but separation of the different DNA pools is almost impossible.

Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin.

Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D).

sp. nov., a novel hexadecane-degrading species isolated from plastic waste.

Strain NGK65, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65 hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0-1% NaCl and at pH 7.

sp. nov., a novel species of the family isolated from plastic waste.

Strain NGK35 is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 µm long and 0.

Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert.

The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.

Greenhouse gas production and lipid biomarker distribution in Yedoma and Alas thermokarst lake sediments in Eastern Siberia.

Permafrost thaw leads to thermokarst lake formation and talik growth tens of meters deep, enabling microbial decomposition of formerly frozen organic matter (OM). We analyzed two 17-m-long thermokarst lake sediment cores taken in Central Yakutia, Russia. One core was from an Alas lake in a Holocene thermokarst basin that underwent multiple lake generations, and the second core from a young Yedoma upland lake (formed ~70 years ago) whose sediments have thawed for the first time since deposition.

Living Lithic and Sublithic Bacterial Communities in Namibian Drylands.

Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted.

Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter.

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate.

Microbial Signatures in Deep CO-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic).

The Hartoušov mofette system is a natural CO degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO blow out occurred at a depth of 78.

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments.

More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa.

Transitory microbial habitat in the hyperarid Atacama Desert.

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth.

Anaerobic methanotrophic communities thrive in deep submarine permafrost.

Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments.

Cell Membrane Fatty Acid Composition of PB4, Isolated from Antarctic Glacier Forefield Soils, in Response to Changing Temperature and pH Conditions.

Microorganisms in Antarctic glacier forefields are directly exposed to the hostile environment of their habitat characterized by extremely low temperatures and changing geochemical conditions. To survive under those stress conditions microorganisms adapt, among others, their cell membrane fatty acid inventory. However, only little is known about the adaptation potential of microorganisms from Antarctic soil environments.

Membrane Lipids as Indicators for Viable Bacterial Communities Inhabiting Petroleum Systems.

Microbial activity in petroleum reservoirs has been implicated in a suite of detrimental effects including deterioration of petroleum quality, increases in oil sulfur content, biofouling of steel pipelines and other infrastructures, and well plugging. Here, we present a biogeochemical approach, using phospholipid fatty acids (PLFAs), for detecting viable bacteria in petroleum systems. Variations within the bacterial community along water flow paths (producing well, topside facilities, and injection well) can be elucidated in the field using the same technique, as shown here within oil production plants in the Molasse Basin of Upper Austria.

The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems.

Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today.

Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake.

A novel methanogenic archaeon, strain MC-15(T), was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2-4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2.

Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake.

A novel strain of methanogenic archaea, designated MC-20(T), was isolated from the anoxic sediment of a subsurface lake in Movile Cave, Mangalia, Romania. Cells were non-motile, Gram-stain-negative rods 3.5-4.

Herbaspirillum psychrotolerans sp. nov., a member of the family Oxalobacteraceae from a glacier forefield.

A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1(T) was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1(T) has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1(T) is able to grow between -5 °C and 30 °C with optimum growth at 14-20 °C.

Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil.

A methanogenic archaeon, strain SMA-21(T), was isolated from a permafrost-affected soil by serial dilution in liquid medium. The cells were non-motile, stained Gram-negative and grew as irregular cocci with a diameter of 1.3-2.

Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield.

During diversity studies of the glacier forefields of the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium, designated strain PB4(T) was isolated from a soil sample. Strain PB4(T) produces indole from tryptophan and hydrolyses casein. It grows between 0 and 25 °C with an optimum growth temperature of 20 °C.

Physiological and proteomic adaptation of "Aromatoleum aromaticum" EbN1 to low growth rates in benzoate-limited, anoxic chemostats.

"Aromatoleum aromaticum" EbN1 was cultivated at different growth rates in benzoate-limited chemostats under nitrate-reducing conditions. Physiological characteristics, proteome dynamics, phospholipid-linked fatty acid (PLFA) composition, and poly(3-hydroxybutyrate) (PHB) content were analyzed in steady-state cells at low (μ(low)) (0.036 h(-1)), medium (μ(med)) (0.

Leifsonia psychrotolerans sp. nov., a psychrotolerant species of the family Microbacteriaceae from Livingston Island, Antarctica.

A cold-tolerant, yellow-pigmented, Gram-positive, motile, facultatively anaerobic bacterial strain, LI1(T), was isolated from a moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St. Kliment Ohridski. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Leifsonia kafniensis KFC-22(T), Leifsonia pindariensis PON10(T) and Leifsonia antarctica SPC-20(T), with which it showed sequence similarities of 99.

Cryobacterium arcticum sp. nov., a psychrotolerant bacterium from an Arctic soil.

A psychrotolerant, Gram-stain-positive, yellow-pigmented, aerobic rod, designated SK1(T), was isolated from a soil sample collected from Store Koldewey, north-east Greenland. Cells were catalase- and methyl red-positive, produced H(2)S and produced acid from glucose, mannitol and salicin. Strain SK1(T) was able to grow between -6 and 28 °C, with an optimum at 20 °C.

Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil.

Two novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2(T) and LI3(T), were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod-coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2(T) (97.

Estimation of bacterial biomass in subsurface sediments by quantifying intact membrane phospholipids.

In an earlier study of deep subsurface sediments from Nankai Trough (ODP Leg 190, offshore Japan) we employed intact phospholipids (PLs) as molecular indicators of living microorganisms. The current study extends this work by quantifying absolute amounts of sedimentary PLs by liquid chromatography-mass spectrometry (LC-MS) and by converting PL data into cell numbers in order to improve methods to estimate the extent of bacterial life in the subsurface. Investigations were carried out on 90 cm short cores of Lake Baikal sediment.