Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

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MetaSPAdes: A new versatile metagenomic assembler

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Halogenated inorganic complexes Ax[MHaly] (A = alkali metal or alkaline earth, M = transition or main group metal, x = 1–3, and y = 2–9) are an archetypal class of compounds that provide entry points to large areas of inorganic and physical chemistry. All of the hexahalo complexes adopt an octahedral, Oh, symmetry (or nearly so). Consequently, one of the bending modes is forbidden in both the infrared and Raman spectra. In the solid state, many of the complexes crystallize in the cubic space group Fm3̅m, which preserves the octahedral symmetry. Even for those that are not cubic, the octahedral symmetry of the [MHal6]n− ion is largely retained and, to a good approximation, so are the selection rules. In the present work, we show that by using the additional information provided by neutron vibrational spectroscopy, in combination with conventional optical spectroscopies, we can generate complete and unambiguous assignments for all the modes. Comparison of the experimental and calculated transition energies for the systems where periodic-density functional theory was possible (i.e., those for which the crystal structure is known) shows that the agreement is almost quantitative. We also provide a linear relationship that enables the prediction of the forbidden mode.

Vibrational Spectroscopy of Hexahalo Complexes

of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. The Global Importance of Subsurface Microbial Communities We stand on the cusp of a much deeper grasp of subsurface microbes as agents of biogeochemistry than has ever been achieved before. An understanding of subsurface microbial communities is important at this juncture because the subsurface remains poorly represented in current models of biogeochemical processes, while DNA sequencing and mass spectrometric capabilities now position us to explore this topic comprehensively via metagenomics, metatranscriptomics, and metaproteomics [1–6]. By ‘subsurface’ we mean that part of the earth below the surface of the terrestrial landscape. As a practical matter, this paper is focused on the shallow subsurface, which we arbitrarily define as <10 m below the terrestrial surface. The practical and scientific implications of understanding microbial community structure and interactions among species at a mechanistic level, including species present at <0.1% of the community, in this environment are enormous [7,8]. These include greatly improved ability to (i) estimate greenhouse gas fluxes to and from the subsurface via modeling of microbially driven Trends

https://www.cell.com/trends/microbiology/pdf/S0966-842X(16)30020-8.pdf

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical

Improving the predictive capabilities of the river corridor and watershed hydro-biogeochemistry across the watershed scale requires overcoming several underlying challenges, such as implementing an appropriate model structure as well as applying adequate parameters and meeting significant computational demands. To address these challenges, we developed a scale-adaptive framework: a cascade of process integration from a meander to the floodplain to the sub-watershed and watershed scales to compute geochemical exports and river water quality as a function of the characteristic watershed features, such as topography, wetness index, meanders, sinuosity, and amplitudes. To demonstrate our approach, we conducted this study at the East River Watershed, the study site of Berkeley Lab's Watershed Function Scientific Focus Area. We modeled a floodplain with 10-meander and 2-meander systems using PFLOTRAN—an open-source, high-resolution, three-dimensional, reactive flow, and transport code—and then developed scaling relationships in the East River Watershed. We developed the RiverFlotran Module and integrated it with PFLOTRAN to account for the bi-directional exchange of geochemical species and quantify river water quality changes. The RiverFlotran module uses the fully dynamic 1D shallow-water equations. We integrated a complex biotic and abiotic reaction network, representing heterotrophic and chemolithoautotrophic pathways and precipitation and dissolution of various minerals, into PFLOTRAN. The model results indicated that the East River floodplain

Developing insights into river corridor and watershed hydro-biogeochemistry across scales

Determine if biostimulation of alluvial aquifers by electron donor amendment can effectively remove U(VI) from groundwater at the field scale. Uranium contamination in groundwater is a significant problem at several DOE sites. In this project, the possibility of accelerating bioreduction of U(VI) to U(IV) as a means of decreasing U(VI) concentrations in groundwater is directly addressed by conducting a series of field-scale experiments. Scientific goals include demonstrating the quantitative linkage between microbial activity and U loss from groundwater and relating the dominant terminal electron accepting processes to the rate of U loss. The project is currently focused on understanding the mechanisms for unexpected long-term ({approx}2 years) removal of U after stopping electron donor amendment. Results obtained in the project successfully position DOE and others to apply biostimulation broadly to U contamination in alluvial aquifers.

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Subsurface Biogeochemical Heterogeneity (Field-scale removal of U(VI) from groundwater in an alluvial aquifer by electron donor amendment)

A laboratory scale experiment was conducted to examine the use of induced polarization and electrical conductivity to monitor microbial induced sulfide precipitation under anaerobic conditions in sand filled columns. Three columns were fabricated; one for electrical measurements, one for geochemical sampling and a third non-inoculated column was used as a control. A continual upward flow of nutrients and metals in solution was established in each column. Desulfovibrio vulgaris microbes were injected into the middle of the geochemical and electrical columns. Iron and zinc sulfides precipitated along a microbial action front as a result of sulfate reduction due by Desulfovibrio vulgaris. The precipitation front initially developed near the microbial injection location, and subsequently migrated towards the nutrient inlet, as a result of chemotaxis by Desulfovibrio vulgaris. Sampling during and subsequent to the experiment revealed spatiotemporal changes in the biogeochemical measurements associated with microbial sulfate reduction. Conductivity measurements were insensitive to all biogeochemical changes occurred within the column. Changes in the IP response (of up to 14 mrad)were observed to coincide in place and in time with the active microbe respiration/sulfide precipitation front as determined from geochemical sampling. The IP response is correlated with the lactate concentration gradient, an indirect measurement ofmore » microbial metabolism, suggesting the potential of IP as a method for monitoring microbial respiration/activity. Post experimental destructive sample analysis and SEM imaging verified the geochemical results and supported our hypothesis that microbe induced sulfide precipitation is directly detectable using electrical methods. Although the processes not fully understood, the IP response appears to be sensitive to this anaerobic microbial precipitation, suggesting a possible novel application for the IP method.« less

/pdf/induced-polarization-response-of-microbial-induced-16oaxn02dz.pdf

Kenneth H. Williams

Papers

Vibrational Spectroscopy of Hexahalo Complexes

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical

Developing insights into river corridor and watershed hydro-biogeochemistry across scales

Subsurface Biogeochemical Heterogeneity (Field-scale removal of U(VI) from groundwater in an alluvial aquifer by electron donor amendment)

Induced polarization response of microbial induced sulfideprecipitation