Biology subjects

Van Goethem, M. W.

Publications and source records attributed to Van Goethem, M. W..

6 recordsLinked to original sources

bioRxiv2021

Hybrid Clustering of Long and Short-read for Improved Metagenome Assembly

Next-generation sequencing has enabled metagenomics, the study of the genomes of microorganisms sampled directly from the environment without cultivation. We previously developed a proof-of-concept, scalable metagenome clustering algorithm based on Apache Spark to cluster sequence reads according to their species of origin. To overcome its under-clustering problem on short-read sequences, in this study we developed a new, two-step Label Propagation Algorithm (LPA) that first forms clusters of long reads and then recruits short reads to these clusters. Compared to alternative label propagation strategies, this hybrid clustering algorithm (hybrid-LPA) yields significantly larger read clusters without compromising cluster purity. We show that adding an extra clustering step before assembly leads to improved metagenome assemblies, predicting more complete genomes or gene clusters from a synthetic metagenome dataset and a real-world metagenome dataset, respectively. These results suggest that hybrid-LPA is a good alternative to current metagenome assembly practice by providing benefits in both scalability and accuracy on large metagenome datasets. Availability and implementationhttps://bitbucket.org/zhong_wang/hybridlpa/src/master/. Contactzhongwang@lbl.gov

bioinformatics↗

bioRxiv2021

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 695 novel, full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night in cyanobacteria but not in other phyla, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

genomics↗

bioRxiv2020

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing

The microbiome plays a central role in biochemical cycling and nutrient turnover of most ecosystems. Because it can comprise myriad microbial prokaryotes, eukaryotes and viruses, microbiome characterization requires high-throughput sequencing to attain an accurate identification and quantification of such co-existing microbial populations. Short-read next-generation-sequencing (srNGS) revolutionized the study of microbiomes and remains the most widely used approach, yet read lengths spanning only a few of the nine hypervariable regions of the 16S rRNA gene limit phylogenetic resolution leading to misclassification or failure to classify in a high percentage of cases. Here we evaluate a synthetic long-read (SLR) NGS approach for full-length 16S rRNA gene sequencing that is high-throughput, highly accurate and low-cost. The sequencing approach is amenable to highly multiplexed sequencing and provides microbiome sequence data that surpasses existing short and long-read modalities in terms of accuracy and phylogenetic resolution. We validated this commercially-available technology, termed LoopSeq, by characterizing the microbial composition of well-established mock microbiome communities and diverse real-world samples. SLR sequencing revealed differences in aquatic community complexity associated with environmental gradients, resolved species-level community composition of uterine lavage from subjects with histories of misconception and accurately detected strain differences, multiple copies of the 16S rRNA in a single strains genome, as well as low-level contamination in soil cyanobacterial cultures. This approach has implications for widespread adoption of high-resolution, accurate long-read microbiome sequencing as it is generated on popular short read sequencing platforms without the need for additional infrastructure.

microbiology↗

bioRxiv2020

A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms

A surprising diversity and abundance of microorganisms resides in the cold desert soils of Antarctica. The metabolic processes that sustain them, however, are poorly understood. In this study, we used metagenomic and biogeochemical approaches to study the microbial communities in 16 physicochemically diverse mountainous and glacial soils from remote sites in South Victoria Land, north of the Mackay Glacier. We assembled 451 metagenome-assembled genomes from 18 bacterial and archaeal phyla, constituting the largest resource of Antarctic soil microbial genomes to date. The most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen and carbon monoxide to meet energy, carbon, and, through metabolic water production, hydration needs. Phylogenetic analysis and structural modelling infer that bacteria from nine phyla can scavenge atmospheric hydrogen using a previously unreported enzyme family, the group 1l [NiFe]-hydrogenases. Consistently, gas chromatography measurements confirmed most soils rapidly consume atmospheric hydrogen and carbon monoxide, and provide the first experimental evidence of methane oxidation in non-maritime Antarctica. We also recovered genomes of microorganisms capable of oxidizing other inorganic compounds, including nitrogen, sulfur, and iron compounds, as well as harvesting solar energy via photosystems and novel microbial rhodopsins. Bacterial lineages defined by symbiotic lifestyles, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also surprisingly abundant. We conclude that the dominant microorganisms in Antarctic soils adopt mixotrophic strategies for energy and sometimes carbon acquisition, though they co-exist with diverse bacteria and archaea that adopt more specialist lifestyles. These unprecedented insights and associated genome compendium will inform efforts to protect biodiversity in this continent.

microbiology↗

bioRxiv2020

Nutrient parsimony shapes diversity and functionality in hyper-oligotrophic Antarctic soils

The balance of nutrients in soil is critical for microbial growth and function, and stoichiometric values below the Redfield ratio for C:N:P can negatively affect microbial ecosystem services. However, few studies have assessed the relationships between nutrient balance and biological productivity in extremely nutrient-poor habitats. The Mackay Glacier region of Eastern Antarctica is a hyper-oligotrophic ice-free desert and is an appropriate landscape to evaluate the effects of nutrient deficiency and imbalance on microbial community ecology. In a survey of multiple, widely dispersed soil samples from this region, we detected only low rates of microbial respiration, and observed that C:N:P ratios were well below those required for optimal activity. In silico metagenomic and soil isotopic ratio ({delta}15N) analyses indicated that the capacity for nitrogen fixation was low, but that soil microbial communities were enriched for soil nitrate assimilation processes, mostly associated with heterotrophic taxa.{delta} 13C isotope ratio data suggested that carbon dioxide was fixed principally via the Calvin cycle. Genes involved in this pathway were common to all metagenomes and were primarily attributed to members of the dominant soil bacterial phyla: Bacteroidetes and Acidobacteria. The identification of multiple genes encoding non-photoautotrophic RUBISCO and carbon dioxide dehydrogenase enzymes in both the metagenomic sequences and assembled MAGs is suggestive of a trace-gas scavenging physiology in members of these soil communities.

ecology↗

bioRxiv2017

Assembling Metagenomes, One Community At A Time

Metagenomics allows unprecedented access to uncultured environmental microorganisms. The assembly of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes of dominant taxa, including uncultured members of a community. However, while numerous platforms have been developed for this critical step, there is currently no strict standard for the assembly of metagenomic sequence data. To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of eight prominent assembly tools on nine publicly-available environmental metagenomes. We found that assembler choice ultimately hinges on the scientific question at hand, the resources available and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.

bioinformatics↗