Investigation of the presence of an aliphatic biopolymer in cyanobacteria: Implications for kerogen formation

Algaenan has been suggested to be one of the main precursors of certain kerogens. It is a non-hydrolysable and insoluble biomolecule of high molecular weight. It has been found in a limited number of microalgae species. There is considerable uncertainty about its formation and preservation, as well as its role in kerogen formation and the implications for the global C cycle. We tested whether the cyanobacterium Chlorogloeopsis fritschii can synthesise a biomacromolecule similar to algaenan with potential to contribute to kerogen via selective preservation. Two freshwater green microalgae, Pseudochoricystis ellipsoidea and Scenedesmus obliquus, as well as C. fritschii, were subjected to harsh solvent extraction and hydrolysis steps to obtain an insoluble and non-hydrolysable macromolecule. The residues from all three species were analysed using pyrolysis–gas chromatography–mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. The analysis revealed that C. fritschii indeed contains a resistant biomacromolecule exhibiting the characteristic aliphatic structure of algaenan, similar to the algaenan residues from the two microalgae. Due to the robust nature of Chlorogloeopsis compared with eukaryotes, it can prevail in extreme environmental conditions such as freezing, thawing, desiccation and overheating – conditions prevalent on the primeval earth. The presence of a resistant aliphatic biopolymer in Chlorogloeopsis suggests that cyanobacteria could have contributed to kerogen via selective preservation

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah.

A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity

SummaryThe selective inhibition of bacterial β-glucuronidases was recently shown to alleviate drug-induced gastrointestinal toxicity in mice, including the damage caused by the widely used anticancer drug irinotecan. Here, we report crystal structures of representative β-glucuronidases from the Firmicutes Streptococcus agalactiae and Clostridium perfringens and the Proteobacterium Escherichia coli, and the characterization of a β-glucuronidase from the Bacteroidetes Bacteroides fragilis. While largely similar in structure, these enzymes exhibit marked differences in catalytic properties and propensities for inhibition, indicating that the microbiome maintains functional diversity in orthologous enzymes. Small changes in the structure of designed inhibitors can induce significant conformational changes in the β-glucuronidase active site. Finally, we establish that β-glucuronidase inhibition does not alter the serum pharmacokinetics of irinotecan or its metabolites in mice. Together, the data presented advance our in vitro and in vivo understanding of the microbial β-glucuronidases, a promising new set of targets for controlling drug-induced gastrointestinal toxicity

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

NCBI’s virus discovery codeathon: building “FIVE” —the Federated Index of Viral Experiments API index

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE

Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces

We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence

Hydrogen-isotopic variability in fatty acids from Yellowstone National Park hot spring microbial communities

We report the abundances and hydrogen-isotopic compositions (D/H ratios) of fatty acids extracted from hot-spring microbial mats in Yellowstone National Park. The terrestrial hydrothermal environment provides a useful system for studying D/H fractionations because the numerous microbial communities in and around the springs are visually distinct, separable, and less complex than those in many other aquatic environments. D/H fractionations between lipids and water ranged from −374‰ to +41‰ and showed systematic variations between different types of microbial communities. Lipids produced by chemoautotrophic hyperthermophilic bacteria, such as icosenoic acid (20:1), generally exhibited the largest and most variable fractionations from water (−374‰ to −165‰). This was in contrast to lipids characteristic of heterotrophs, such as branched, odd chain-length fatty acids, which had the smallest fractionations (−163‰ to +41‰). Mats dominated by photoautotrophs exhibited intermediate fractionations similar in magnitude to those expressed by higher plants. These data support the hypothesis that variations in lipid D/H are strongly influenced by central metabolic pathways. Shifts in the isotopic compositions of individual fatty acids across known ecological boundaries show that the isotopic signature of specific metabolisms can be recognized in modern environmental samples, and potentially recorded in ancient ones. Considering all sampled springs, the total range in D/H ratios is similar to that observed in marine sediments, suggesting that the trends observed here are not exclusive to the hydrothermal environment