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The article focuses on the triggers behind toxic cyanobacterial blooms in Missisquoi Bay on Lake Champlain using quantitative polymerase chain reaction and next-generation sequencing. It states that non-point sources are responsible for high concentrations of nitrogen and phosphorus in the bay, with nutrient concentrations and total phosphorus:total nitrogen ratios approaching 1:11, along with warmer temperatures, promote the blooms. It correlates total and dissolved phosphorus with rainfall.

Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants. [ABSTRACT FROM AUTHOR]

Examines the use of genomics-based tools for the complete nucleotide sequencing from both prokaryotic and eukaryotic organisms. Importance of genetic code for the sequence of DNA; Identification of the alkane degradation genes from Mycobacterium tuberculosis; Application of microarray technology.

Climate warming and subsequent permafrost thaw may result in organic carbon and nutrient stores being metabolized by microbial communities, resulting in a positive feedback loop of greenhouse gas (GHG) soil emissions. As the third most important GHG, understanding nitrous oxide (N2O) flux in Arctic mineral ice-wedge polygon cryosols and its relationship to the active microbial community is potentially a key parameter for understanding future GHG emissions and climatic warming potential. In the present study, metatranscriptomic analyses of active layer Arctic cryosols, at a representative ice-wedge polygon site, identified active nitrogen-fixing and denitrifying bacteria that included members of Rhizobiaceae, Nostocaceae, Cyanothecaceae, Rhodobacteraceae, Burkholderiaceae, Chloroflexaceae, Azotobacteraceae and Ectothiorhodospiraceae. Unique microbial assemblages with higher proportion of Rhodobacteriales and Rhocyclales were identified by targeted functional gene sequencing at locations with higher (P = 0.053) N2O emissions in the wetter trough soils compared with the dryer polygon interior soils. This coincided with a higher relative abundance of the denitrification nirS gene and higher nitrate/nitrite concentrations in trough soils. The elevated N2O flux observed from wetter trough soils compared with drier polygon interior soils is concerning from a climate warming perspective, since the Arctic is predicted to become warmer and wetter. [ABSTRACT FROM AUTHOR]

The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (-5°C), hypersalinity (salinity, 24%), and reducing (≈-165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day-1). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments. [ABSTRACT FROM AUTHOR]

Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for 2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [15N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using lage-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in 15N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments. [ABSTRACT FROM AUTHOR]

Abstract: The study of ancient massive ground ice and sediment-rich ice bodies not only allows an understanding of the stability of permafrost, but also offers the possibility to understand the long-term preservation and viability of microbes within these ice bodies. Although microorganisms have been identified in ancient bodies of ground ice and permafrost, there still is a lack of convincing evidence that the microbes were metabolically active within the ice. In this study, we combine geomicrobiology methods with the measurements of occluded gasses in four ancient massive ground ice bodies to provide evidence of microbial respiration. In our samples, abundant cold-adapted heterotroph microorganisms were identified using culture-dependent and -independent methods. The occluded gas measurements, with low δ(O2/Ar) (less than −21.4%) and δ13CCO2 (as low as −25.2‰) values and high δ18OO2 (up to +16.3‰) values are suggestive of in situ consumption of O2 by heterotrophic psychrophilic bacteria living within the ice matrix. Overall, the multi-disciplinary approach provides a strong set of tools from which to infer metabolic activity within bodies of ground ice. The analysis of δ(O2/Ar), δ18OO2 and δ13CCO2 from occluded gasses in ice are strong isotope biosignatures that could allow detecting evidence of life on other planetary icy bodies such as Mars. [Copyright &y& Elsevier]

The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills., Competing Interests: Authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO 2 and CH 4 fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH 4 and CO 2 flux at a high Arctic ice-wedge polygon terrain site, with higher CO 2 emissions and lower CH 4 uptake at troughs compared to polygon interior soils. The pmoA sequencing suggested that USCα cluster of uncultured methanotrophs is likely responsible for observed methane sink. Community profiling revealed distinct assemblages across the terrain at different depths. Deeper soils contained higher abundances of Verrucomicrobia and Gemmatimonadetes, whereas the polygon interior had higher Acidobacteria and lower Betaproteobacteria and Deltaproteobacteria abundances. Genome sequencing of isolates from the terrain revealed presence of carbon cycling genes including ones involved in serine and ribulose monophosphate pathways. A novel hybrid network analysis identified key members that had positive and negative impacts on other species. Operational Taxonomic Units (OTUs) with numerous positive interactions corresponded to Proteobacteria, Candidatus Rokubacteria and Actinobacteria phyla, while Verrucomicrobia and Acidobacteria members had negative impacts on other species. Results indicate that topography and microbial interactions impact community composition., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at -15 °C, the lowest temperature demonstrated to date, and is metabolically active at -25 °C in frozen permafrost microcosms. To understand how P. halocryophilus Or1 remains active under the subzero and osmotically dynamic conditions that characterize its native permafrost habitat, we investigated the genome, cell physiology and transcriptomes of growth at -15 °C and 18% NaCl compared with optimal (25 °C) temperatures. Subzero growth coincides with unusual cell envelope features of encrustations surrounding cells, while the cytoplasmic membrane is significantly remodeled favouring a higher ratio of saturated to branched fatty acids. Analyses of the 3.4 Mbp genome revealed that a suite of cold and osmotic-specific adaptive mechanisms are present as well as an amino acid distribution favouring increased flexibility of proteins. Genomic redundancy within 17% of the genome could enable P. halocryophilus Or1 to exploit isozyme exchange to maintain growth under stress, including multiple copies of osmolyte uptake genes (Opu and Pro genes). Isozyme exchange was observed between the transcriptome data sets, with selective upregulation of multi-copy genes involved in cell division, fatty acid synthesis, solute binding, oxidative stress response and transcriptional regulation. The combination of protein flexibility, resource efficiency, genomic plasticity and synergistic adaptation likely compensate against osmotic and cold stresses. These results suggest that non-spore forming P. halocryophilus Or1 is specifically suited for active growth in its Arctic permafrost habitat (ambient temp. ∼-16 °C), indicating that such cryoenvironments harbor a more active microbial ecosystem than previously thought.

Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for ∼2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [(15)N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using large-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in (15)N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments.

A novel, moderately halophilic, endospore-forming bacterial strain, designated Hal 1T, was isolated from a permafrost core collected from the Canadian high Arctic. The temperature for growth of strain Hal 1T was 0-30 degrees C with no growth observed at either -5 or 37 degrees C (optimum growth at about 25 degrees C). Strain Hal 1T was able to grow at NaCl concentrations of 0-20% (w/v) and did not have an absolute NaCl requirement for growth; optimal growth was at 5% (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain Hal 1T and the type strains of Virgibacillus carmonensis and Virgibacillus necropolis was 98.2%; values with respect to the type strains of other recognized Virgibacillus species were below 96.0%. The DNA G+C content of strain Hal 1T was 38.2 mol%. Levels of DNA-DNA relatedness between strain Hal 1T and the type strains of V. carmonensis and V. necropolis were 14.0 and 21.0%, respectively. The major fatty acid of strain Hal 1T was anteiso-C15:0, consistent with species of the genus Virgibacillus. The cell-wall peptidoglycan of strain Hal 1T was type A1alpha and the major respiratory quinone was MK-7. On the basis of genotypic and physiological results, strain Hal 1T (=DSM 19574T=JCM 14839T) is proposed as the type strain of a novel species of the genus Virgibacillus, namely Virgibacillus arcticus sp. nov.

A Gram-positive, aerobic, rod-shaped bacterium (strain Eur1 9.5(T)) was isolated from a 9-m-deep permafrost sample from the Canadian high Arctic. Strain Eur1 9.5(T) could not be cultivated in liquid medium and grew over the temperature range 5-37 degrees C; no growth was observed at 42 degrees C and only slow growth was observed at 5 degrees C following 1 month of incubation. Eur1 9.5(T) grew over the pH range 5.5-8.9 and tolerated NaCl concentrations of 0-0.5 % (w/v). Eur1 9.5(T) grew heterotrophically on complex carbon substrates and chemolithoautotrophically on inorganic sulfur compounds, as demonstrated by growth on sodium thiosulfate and sulfite as sole electron donors. Eur1 9.5(T) contained iso-C(15 : 0) as the major cellular fatty acid and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1gamma. The DNA G+C content was 53.1 mol%. The 16S rRNA gene sequence of strain Eur1 9.5(T) was only distantly related (

A molecular characterization of pristine and petroleum hydrocarbon-contaminated Alpine soils sampled in Tyrol (Austria) was performed. To identify predominant bacteria, PCR-amplified 16S rRNA gene fragments from five pristine and nine contaminated soils were analysed using denaturing gradient gel electrophoresis (DGGE). Sequencing and phylogenetic analyses demonstrated that the majority of the DGGE bands represented bacteria in the Actinobacteria and Proteobacteria phyla: 18 and 73%, respectively, in pristine soils, compared with 20 and 76%, respectively, in contaminated soils. A different distribution pattern of bacterial classes in the Proteobacteria was observed between pristine and contaminated soils. The relative proportion of microorganisms belonging to the Alphaproteobacteria was larger in pristine (46%) than in contaminated (24%) soils, while Betaproteobacteria and Gammaproteobacteria were detected only in the hydrocarbon-contaminated soils. This result compared favourably with earlier work in which hydrocarbon-degradation genotypes, largely pseudomonads and Acinetobacter, belonging to the Gammaproteobacteria, were enriched following oil hydrocarbon contamination. In contrast, members of the Actinobacteria phylum, represented by Rhodococcus and Mycobacterium, were found in pristine soils where contamination events had not occurred. The results demonstrate a significant shift in the microbial community structure in Alpine soils following contamination. Furthermore, more potentially novel phylotypes were found in the pristine soils than in the contaminated soils.