Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities.

Background: Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia.

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time.

Microbial Communities of Artisanal Fermented Milk Products from Russia.

Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia.

Novel hyperthermophilic crenarchaeon Infirmifilum lucidum gen. nov. sp. nov., reclassification of Thermofilum uzonense as Infirmifilum uzonense comb. nov. and assignment of the family Thermofilaceae to the order Thermofilales ord. nov.

A novel hyperthermophilic crenarchaeon, strain 3507LT, was isolated from a terrestrial hot spring near Tinguiririca volcano, Chile. Cells were non-motile thin, slightly curved filamentous rods. It grew at 73-93 °C and pH range of 5 to 7.

Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium.

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO), with CO/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N/CO-saturated liquid medium and microoxic (2% O) headspace.

Hot in Cold: Microbial Life in the Hottest Springs in Permafrost.

Chukotka is an arctic region located in the continuous permafrost zone, but thermal springs are abundant there. In this study, for the first time, the microbial communities of the Chukotka hot springs (CHS) biofilms and sediments with temperatures 54-94 °C were investigated and analyzed by NGS sequencing of 16S rRNA gene amplicons. In microbial mats (54-75 °C), phototrophic bacteria of genus dominated (up to 89% of all prokaryotes), while were the most numerous at higher temperatures in Fe-rich sediments and filamentous "streamers" (up to 92%).

Tenuifilum thalassicum gen. nov., sp. nov., a novel moderate thermophilic anaerobic bacterium from a Kunashir Island shallow hot spring representing a new family Tenuifilaceae fam. nov. in the class Bacteroidia.

A novel anaerobic moderately thermophilic bacterium, designated strain 38H-str, was isolated from a 12m deep hot spring of the Kunashir Island shore. Gram-negative cells were non-spore-forming, motile, straight or curved filamentous rods, occasionally forming loops and knots. The strain grew at 20-65°C and pH range of 4.

sp. nov., a bacterium isolated from Chukotka hot spring, Arctic region, Russia.

A moderately thermophilic, neutrophilic, aerobic, Gram-negative bacterium, strain 3729k, was isolated from a thermal spring of the Chukotka Peninsula, Arctic region, Russia. It grew chemoorganoheterotrophically, utilizing proteinaceous substrates, including highly rigid keratins as well as various polysaccharides (glucomannan, locust bean gum, gum guar and xanthan gum). The major fatty acids of strain 3729k were iso-C (60.

The first crenarchaeon capable of growth by anaerobic carbon monoxide oxidation coupled with H production.

The ability to grow by anaerobic CO oxidation with production of H from water is known for some thermophilic bacteria, most of which belong to Firmicutes, as well as for a few hyperthermophilic Euryarchaeota isolated from deep-sea hydrothermal habitats. A hyperthermophilic, neutrophilic, anaerobic filamentous archaeon strain 1505=VKM B-3180=KCTC 15798 was isolated from a terrestrial hot spring in Kamchatka (Russia) in the presence of 30% CO in the gas phase. Strain 1505 could grow lithotrophically using carbon monoxide as the energy source with the production of hydrogen according to the equation CO+HO→CO+H; mixotrophically on CO plus glucose; and organotrophically on peptone, yeast extract, glucose, sucrose, or Avicel.

Novel Hyperthermophilic Crenarchaeon sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis.

A novel hyperthermophilic, anaerobic filamentous archaeon, strain 1910b, is capable of growing with cellulose as its sole carbon and energy source. This strain was isolated from a terrestrial hot spring in Kamchatka, Russia. The isolate 1910b grew optimally at a temperature of 80°C and a pH of 5.

gen. nov., sp. nov., a moderately thermophilic bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, , which includes the previously uncultivated lineage OLB14.

A novel aerobic moderately thermophilic bacterium, strain 3753O, was isolated from a Chukotka hot spring (Arctic, Russia) using the newly developed technology of laser engineering of microbial systems. Сells were regular short rods, 0.4×0.

'Candidatus Oscillochloris fontis': a novel mesophilic phototrophic Chloroflexota bacterium belonging to the ubiquitous Oscillochloris genus.

We present the results of a study of mesophilic anoxygenic phototrophic Chloroflexota bacteria from Mechigmen hot spring (the Chukotka Peninsula) and Siberia. According to 16S rRNA phylogenetic analysis, these bacteria belong to Oscillochloris trichoides. However, sequencing the draft genome of the bacterium from the Chukotka and analysis of the average nucleotide identity, as well as in silico DNA-DNA hybridization, reveal that this bacterium belongs to a novel species within the Oscillochloris genus.

gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring.

An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain 1633, was isolated from a terrestrial hot spring of the Uzon Caldera (Kamchatka Peninsula, Russia). Cells were regular cocci, 0.5-0.

Complete genome sequence of the hyperthermophilic cellulolytic crenarchaeon "Thermogladius cellulolyticus" 1633.

Strain 1633, a novel member of the genus Thermogladius, isolated from a freshwater hot spring, is an anaerobic hyperthermophilic crenarchaeon capable of fermenting proteinaceous and cellulose substrates. The complete genome sequence reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof pathway for glucose metabolism, cytoplasmic NADP-dependent hydrogenase, and several energy-coupling membrane-bound oxidoreductases.

Anaerobic transformation of carbon monoxide by microbial communities of Kamchatka hot springs.

Carbon monoxide (CO) is one of the common gaseous compounds found in hot volcanic environments. It is known to serve as the growth substrate for a number of thermophilic prokaryotes, both aerobic and anaerobic. The goal of this work was to study the process of anaerobic transformation of CO by microbial communities inhabiting natural thermal environments: hot springs of Uzon Caldera, Kamchatka.