Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples

Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses—bacteriophages and archaeal viruses—influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage–host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth’s ecosystems.

mOTUpan: a robust Bayesian approach to leverage metagenome assembled genomes for core-genome estimation

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome assembled genomes (MAGs) or single-cell assembled genomes (SAGs). While this expanded diversity can provide novel insights about microbial population structure, most tools available for core-genome estimation are overly sensitive to genome completeness. Consequently a major portion of the huge phylogenetic diversity uncovered by environmental genomics approaches remain excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core-genome for sets of genomes of highly diverse completeness range. The likelihood for each gene-cluster to belong to core- or accessory-genome is estimated by computing the probability of its presence/absence pattern in the target set of genomes. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates as state-of-the-art tools Roary and PPanGGoLiN for high-quality genomes and outperforms them at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.

Environmental genomics points to non-diazotrophic Trichodesmium species abundant and widespread in the open ocean

Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton primary productivity at large-scale. Here, we report the genome-resolved metagenomic characterization of two newly identified marine species we tentatively named Ca. Trichodesmium miru and Ca. Trichodesmium nobis. Near-complete environmental genomes for those closely related candidate species revealed unexpected functional features including a lack of the entire nitrogen fixation gene apparatus and hydrogen recycling genes concomitant with the enrichment of nitrogen assimilation genes and apparent acquisition of the nirb gene from a non-cyanobacterial lineage. These comparative genomic insights were cross-validated by complementary metagenomic investigations. Our results contrast with the current paradigm that Trichodesmium species are necessarily capable of nitrogen fixation. The black queen hypothesis could explain gene loss linked to nitrogen fixation among Trichodesmium species, possibly triggered by gene acquisitions from the colony epibionts. Critically, the candidate species are not only widespread in the 3-2000 micron planktonic size fraction of the surface of the oceans and seas, but might also substantially expand the ecological niche of Trichodesmium, stressing the need to disconnect taxonomic signal for this genus from the ability of a microbial community to fix nitrogen. Especially, differentiating diazotrophic from non-diazotrophic populations when counting Trichodesmium filaments and colonies might help refine our understanding of the marine nitrogen balance. While culture representatives are needed to move beyond metagenomic insights, we are reminded that established links between taxonomic lineages and functional traits might not always hold true.

Environmental Genomics Applications for Environmental Management Activities in the Oil and Gas Industry - State of the Art Review and Future Research Needs

The International Association of Oil and Gas Producers (IOGP) Environmental Genomics Joint Industry Program (JIP) was formed in June 2019. The aim of the JIP is to facilitate the development of guidelines for the application of environmental genomics to support environmental management activities in the oil and gas industry. Towards this goal, a white paper summarizing the state-of-the-art in environmental genomics research and how it may be used to advance technology development opportunities for the oil and gas industry was drafted. More specifically, a series of applications and focus areas of primary interest to oil and gas companies were covered including: baseline assessments; detection of key species; rapid assessment of invasive species; population status and dynamics; monitoring of environmental effects of oil and gas activities; remediation and restoration; sampling design; data analysis and interpretation; community representation; species abundance, distribution and viability; and real-time on-site measurement and analysis. baseline assessments; detection of key species; rapid assessment of invasive species; population status and dynamics; monitoring of environmental effects of oil and gas activities; remediation and restoration; sampling design; data analysis and interpretation; community representation; species abundance, distribution and viability; and real-time on-site measurement and analysis. In addition to the literature review, consultation of professionals from academic, regulatory, and industrial backgrounds with expertise on these topics was conducted. While there was a consensus that the application of environmental genomics has advanced greatly in a short period of time with demonstrable benefit potential, there was acknowledgement that key aspects of best management practices are still lacking. Furthermore, while the majority of regulators interviewed were aware to varying degrees of the methodological limitations which restrict the present use of environmental genomics in regulatory affairs, it transpired that there is considerable appetite and capacity amongst the regulatory community to engage in collaborative research initiatives with the oil and gas industry and academia. Through these academic, regulatory, and industrial consultation, specific environmental genomics study areas and applications requiring further development and refinement were identified. These include: methodological standardization, persistence and dispersal of eDNA; eDNA data integration with various other data types; improvement of reference databases; and refinement of molecular indices. methodological standardization, persistence and dispersal of eDNA; eDNA data integration with various other data types; improvement of reference databases; and refinement of molecular indices. Based on the above and considering the most efficient path to greater regulatory uptake for environmental genomic approaches for the oil and gas industry, the JIP’s recommendation is to pursue a Common-Garden Experiment. Such experiment should seek the involvement and ultimately endorsement from the Regulators marking the path towards wider regulatory acceptance and uptake of eDNA-based approaches.

The Molecular Basis for Life in Extreme Environments

Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understanding its molecular basis in such inhospitable conditions, given that such conditions lead to loss of structural changes and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure–function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.