Biology subjects

Lui, L. M.

Publications and source records attributed to Lui, L. M..

17 recordsLinked to original sources

bioRxiv2026

A complete-genome view of phylum Omnitrophota and a multi-order capacity for very long proteins

Phylum Omnitrophota (formerly candidate division OP3) is represented in public databases almost entirely by metagenome-assembled genomes; GTDB R232 contains two complete Omnitrophota assemblies. We present 176 complete and 53 high-quality Omnitrophota genomes from Oxford Nanopore metagenomes of Fennoscandian deep groundwater and the Baltic Sea water column, an 88-fold expansion of the complete Omnitrophota count. The 229 genomes resolve to 202 distinct species at 95 % ANI; 162 of these have no conspecific match in the 714 NCBI HQ Omnitrophota MAGs. Phylogenomically, 171 of the 176 complete genomes fall in class Gorgyraeia -- which contains the cultured episymbiont Velamenicoccus archaeovorus -- and 5 in Omnitrophia, with multiple Gorgyraeia orders and families represented. Phylum Omnitrophota hosts many very long proteins, with the longest in our corpus reaching 147,155 AA; the long end of the length distribution is concentrated on Gorgyraeia contigs across multiple Gorgyraeia orders. 24-28 % of GTDB-Tk-classified Omnitrophota contigs in the deep-groundwater and Baltic samples host at least one [≥] 10-kAA protein. Across the 916-protein long-protein domain-architecture catalog, 94 % carry transmembrane helices or a signal peptide; the four complete-genome proteins above 100,000 amino acids are all in inner-membrane-anchored architectures, the 147,155-AA protein with 147 TM helices. The 176 complete genomes share a uniform metabolic profile across the dominant orders: intact bacterial peptidoglycan biosynthesis alongside fragmentary TCA, incomplete electron transport, absent aerobic terminal oxidase, and partial cofactor and amino-acid biosynthesis. The profile matches the cultured V. archaeovorus phenotype and is consistent with a host-dependent episymbiotic lifestyle. Hypervariable-region calling across the 229 chromosomes returns 1,909 candidate loci, distributed across 223 of them; ribosomal-protein and EF-Tu / EF-G content sits inside called HVRs on 150 of those 223 (67 %), recovering across the collection the housekeeping-cargo integrations documented in Nielsen (2026b). All genomes, the OrthoFinder supermatrix and its ML tree, the 916-protein giant-protein domain-architecture catalog, and per-step scripts are released as a community resource at Zenodo (DOI [TBD]).

microbiology↗

bioRxiv2026

A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota

The archaeal phylum Nanobdellota (formerly Nanoarchaeota) was previously represented by four complete genomes. We present 208 complete Nanobdellota genomes from Oxford Nanopore metagenomes of the Baltic Sea water column and Fennoscandian groundwater (69-201 m below sea level), rotated to the ORC1/Cdc6 replication origin -- a 52-fold expansion of complete-genome representation. Across the ar53 supermatrix and a Nanobdellota-tuned 71-marker supermatrix on 1,239 taxa, the named GTDB orders within Nanobdellota are recovered as monophyletic clades, including the three orders that dominate our environmental sampling: Woesearchaeales, Pacearchaeales, and the GTDB placeholder order SCGC-AAA011-G17. This is consistent with the existing GTDB R232 order-level circumscription. We retire the SCGC-AAA011-G17 placeholder name, replacing it with a complete-genome-anchored SeqCode nomenclatural chain (Maxwellarchaeales ord. nov., Maxwellarchaeaceae fam. nov., Maxwellarchaeum gen. nov., and Maxwellarchaeum balticum sp. nov.) without altering the order-level circumscription. Pacearchaeales and Maxwellarchaeales retain no central or energy metabolism beyond Form III RuBisCO, PEP synthase, and ferredoxin; Woesearchaeales retains partial glycolysis and a V/A-type ATPase. A 4,262-tip phylogeny of rbcL (the RuBisCO large-subunit gene) identifies nine candidate archaea-to-Patescibacteriota Form III RuBisCO transfer events -- including one to a Baltic Minisyncoccia -- versus two reciprocal candidates, consistent with archaea-to-CPR being the more frequently identified direction in our data. All 256 Nanobdellota genomes (208 complete + 48 high-quality non-circular), the ar71 marker set with its 1,239-taxon ML tree, 154 Nanobdellota-trained HMMs for KEGG-ortholog detection in DPANN proteomes (94 ROBUST), and the 4,262-tip rbcL reference tree are released as a community resource, alongside the full analysis archive -- alignments, intermediate trees, structural predictions, and per-step scripts -- at Zenodo (DOI 10.5281/zenodo.20174424; see Using the resource).

microbiology↗

bioRxiv2026

Actinomarina, resolved

Actinomarina (Ca. Actinomarina minuta) is among the smallest known free-living bacteria and among the most abundant photoheterotrophs in ocean surface waters, yet not a single complete genome has been published for any member of the order Actinomarinales. Here we present 84 complete Actinomarina genomes assembled from Oxford Nanopore metagenomes of the San Francisco Estuary (SFE), together with 29 additional high-quality ([≥]95% complete, <5% contamination, single contig) non-circular assemblies. These genomes define 9 species at 95% ANI, three of which are novel, and represent, to our knowledge, the first complete genomes for the entire Actinomarinales order. An expanded phylogeny incorporating 23 high-quality NCBI genomes and a Casp-actino5 outgroup confirms species boundaries and places NCBI genomes among SFE clades. The pangenome of 9,278 clusters is approaching closure (decay ratio 0.55), with a core genome of 227 single-copy genes (2.4%). Singletons (3,858 clusters, 42%) are concentrated in a tRNA-bounded hypervariable region (HVR) at 85-90% of the chromosome from dnaA -- a similar replicative distance to the HVR recently described in Pelagibacter (7-15% from dnaA; Lui & Nielsen, in preparation) but on the opposite replichore. The HVR is flanked by tRNA genes at both boundaries, and in 32 of 84 genomes, the selenocysteine tRNA (selC) is physically located inside the HVR. All 84 genomes encode selenocysteine tRNA (selC) and the selenocysteine biosynthesis genes selA and selD; the elongation factor selB is present but divergent. This has not been previously reported for Actinomarina. Deep learning selenoprotein prediction (deep-Sep) identifies [~]5 selenoproteins per genome in 69 families, including a selenoprotein form of selD itself. Retention of dedicated Sec biosynthetic machinery serving multiple targets in a genome of [~]1.1 Mbp implies that the catalytic advantage of selenocysteine over cysteine is large enough to justify the cost. KofamScan pathway reconstruction reveals the most extensive set of auxotrophies yet documented from complete genomes in a free-living marine bacterium: arginine, histidine, tryptophan, and thiamine biosynthesis are universally absent, biotin biosynthesis is non-functional (final step absent), and only 5 of 8 TCA cycle steps are retained at the standard detection threshold. Gene order is extensively rearranged between species: no gene adjacency is universal across all 84 genomes. NCBI currently lists 396 Actinomarina genomes, none complete; of the 39 that pass quality thresholds, 41% are misclassified by NCBI, belonging to other genera by GTDB-Tk reclassification.

microbiology↗

bioRxiv2026

Pelagibacter, resolved

Pelagibacter, the largest genus within the SAR11 clade, is the most abundant bacterium in the ocean, yet the vast majority of its species-level diversity remains uncharacterized at the genomic level. Here we present 135 complete Pelagibacter genomes -- the largest such collection assembled to date -- comprising 75 from Oxford Nanopore metagenomes of the San Francisco Estuary (SFE), 31 from a deeply sequenced station within the same transect, and 29 from public databases. These genomes define 52 species at 95% ANI, of which 44 (85%) are taxonomically novel. An expanded phylogeny incorporating 89 additional high-quality NCBI genomes confirms that our collection captures the phylogenetic backbone of the genus, with genomes from Hawaii, Namibia, and the Sargasso Sea nesting within SFE clades. The pangenome is open (14,862 singletons, 62%), driven by two distinct mechanisms. First, a universal hypervariable region (HVR) at a conserved chromosomal position (7-15% from dnaA) is present in all 135 genomes, anchored by tRNA genes at both boundaries (Phe/His and Arg). The HVR carries genome-specific surface polysaccharide biosynthesis genes with a GC age gradient -- highest GC at the tRNA boundaries, lowest in the center -- consistent with a two-ended phage insertion model. Only this HVR is positionally conserved across the genus; the three other hypervariable regions previously described in a single reference genome are not. Second, scattered genomic islands throughout the chromosome contribute the remaining singleton content, including chimeric islands with genes from four bacterial phyla. Biosynthetic pathway reconstruction reveals auxotrophies that are phylogenetically structured, not uniform: biotin, reduced sulfur, and glycine are genus-wide dependencies, while isoleucine, pantothenate, histidine, and glyoxylate cycle capacity vary across lineages with significant phylogenetic clustering. Structural annotation with ESMFold and Foldseek resolved 3,125 hypothetical proteins; 1,222 remain uncharacterized by any method, including a 47-amino-acid protein conserved in two-thirds of all genomes within a fixed operonic context -- independently predicted by two gene callers yet matching nothing in any database. A controlled depth comparison at one station demonstrates that standard metagenome sequencing systematically underestimates Pelagibacter diversity, with three species recovered only at elevated depth and the species count at that station more than doubling (9 vs 4).

microbiology↗

bioRxiv2026

General-purpose embeddings for long-read metagenomic sequences via β-VAE on multi-scale k-mer frequencies

Long-read metagenomics routinely produces millions of assembled contigs, creating a need for methods that organize sequences into biologically meaningful groups across samples and environments. We present a general-purpose compositional embedding for metagenomic sequences based on a {beta}-variational autoencoder ({beta}-VAE) trained on multi-scale k-mer frequencies (1-mers through 6-mers; 2,772 features with centered log-ratio transformation). The embedding compresses each contig into a 384-dimensional vector that preserves local compositional similarity, enabling similarity search and graph-based clustering from sequence composition alone. Through systematic comparison of fifteen models trained on up to 17.4 million contigs (525.5 Gbp) from brackish, terrestrial, and reference genome sources, we find that a small set of curated prokaryotic reference genomes (656,000 contigs) outperforms ten-fold larger domain-specific training sets, and that neither reconstruction loss nor Spearman correlation reliably predicts downstream clustering quality. On nearest-neighbor graphs, flow-based clustering (MCL) markedly outperforms modularity-based methods (Leiden), yielding 12,123 clusters from 154,041 contigs ([≥] 100 kbp) with 99.2% phylum-level purity confirmed by independent marker gene phylogenetics. Multi-method taxonomic annotation achieves 87% coverage and reveals that 16.4% of contigs are eukaryotic--the single largest component invisible to standard prokaryotic annotation tools. The embedding provides a sample-independent coordinate system for organizing metagenomic sequence space at scale.

bioinformatics↗

bioRxiv2026

Contrasting population structures coexist in a strain-resolved estuarine microbiome

Whether co-occurring microbial populations share similar evolutionary dynamics remains poorly understood, because strain-level resolution across many lineages simultaneously has been unachievable from metagenomic assembly. Here we apply 720 Gbp of Nanopore sequencing and the assembler myloasm to a South San Francisco Bay microbiome, recovering 488 high-quality single-contig genomes -- including 328 circular chromosomes -- without manual curation. Strain-level resolution revealed striking contrasts in population structure: Pelagibacter yielded 78 high-quality single contig genomes spanning 18 species with no two sharing >=99% average nucleotide identity (ANI) -- every genome a distinct strain, consistent with phage-driven frequency-dependent selection -- while HIMB114 was nearly monotypic, with 9 of 11 high-quality genomes in a single species, suggesting periodic selection or a recent sweep. Using unsupervised Markov clustering of variational autoencoder embeddings, we assigned 99.3% of contigs >=5 kbp to a taxonomic domain and resolved nearly 50% of the community to species level. The assembly also captured nearly 95,000 viral contigs (>=5 kbp) including 502 giant viruses, novel eukaryotic lineages, and mercury resistance genes reflecting the Bays contamination legacy. These contrasting patterns -- coexisting in a single 10-liter sample -- reveal that fundamentally different evolutionary strategies operate simultaneously within a complex microbiome, a level of resolution not previously demonstrated from de novo assembly. Wed like to note that the results of this study mark a milestone in a 10 year hunt for Torben to get as many complete Pelagibacter genomes from a metagenome as possible.

microbiology↗

bioRxiv2024

Emergence and disruption of cooperativity in a denitrifying microbial community

Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter R12 and Acidovorax 3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO3-) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO3-, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO2-, which disrupts denitrification causing N2O off gassing.

microbiology↗

bioRxiv2024

High-throughput protein characterization by complementation using DNA barcoded fragment libraries

Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we use complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. Although assay effectiveness ranged with respect to source genome, with 41% of expected enzymes recovered, even distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron showed success. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein on an amino acid basis. Among unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seqs utility is demonstrated, with future applications in ecology, health, and engineering.

genomics↗

bioRxiv2024

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent to increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. ORR Castellaniella strains showed a higher degree of genetic diversification than those originating from non-ORR sites, which we attribute to the multitude of extreme stressors faced in the ORR subsurface. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least two decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.

microbiology↗

bioRxiv2023

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal contaminated regions of the Oak Ridge Reservation (ORR) subsurface. This meta-mobilome was compared to one derived from samples collected from unimpacted regions of the ORR subsurface. We assembled 1,615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

microbiology↗

bioRxiv2023

Decomposing a San Francisco Estuary microbiome using long read metagenomics reveals species and species- and strain-level dominance from picoeukaryotes to viruses

Although long read sequencing has enabled obtaining high-quality and complete prokaryotic genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent genomes. These challenges include obtaining enough biomass, high-molecular weight DNA extraction, determining the appropriate depth of sequencing, and bioinformatics challenges to separate closely related genomes. This study focuses on decomposing an estuarine water metagenome from USGS Station 36 in the South San Francisco Bay into its constituent genomes and counting the number of organisms present. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and sequenced the sample with 150 Gbases of nanopore sequencing. With our results, we were able to estimate that there are [~]500 bacteria and archaeal species in our sample, obtain 68 high-quality bins (>90% complete, <5% contamination, [≤]5 contigs, no contigs shorter than 100 Kbases, and all ribosomal and necessary tRNA genes). Since we pre-filtered the sample at 11m and then collected directly on to a 0.1m filter, we also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, complete mitochondrial and chloroplast genomes, and detected [~]40,000 viral populations. This deep analysis of the taxonomy of the sample down to the strain and individual contig level allowed us to find that among picoeukaryotes, prokaryotes, and viruses there are likely only a few strains that comprise most of the species abundances. These results also indicate that to truly decompose a metagenome into its constituent genomes, we likely need 1Tbase of sequencing. If you are reading this preprint, know that this is the paper we wanted to write, but it will likely be shortened for submission to a journal.

microbiology↗

bioRxiv2021

Sustained ability of a natural microbial community to remove nitrate from groundwater

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation. Article Impact StatementGroundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.

ecology↗

bioRxiv2020

A method for achieving complete microbial genomes and better quality bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg.

bioinformatics↗

bioRxiv2019

Selective carbon sources influence the end-products of microbial nitrate respiration

Respiratory and catabolic pathways are differentially distributed in microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end-products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end-products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content and function.

microbiology↗

bioRxiv2019

Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated environments. To provide site assessment for a larger study, we processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater from the ENIGMA Field Research Site at the United States Department of Energy (DOE) Oak Ridge Reservation (ORR). We compared fresh core sediments by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including contaminants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. This environmental systems approach provided detailed site-specific biogeochemical information from the various properties of subsurface media to reveal the influences of solid, liquid, and gas phases. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate- reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. This suggested that groundwater predominantly flowed through preferential paths with high flux and little mixing with water in the interstices of sediment particles, which could impact microbial activity. The abundant clay minerals with high surface area and high water-holding capacity of micro-pores of the fine clay rich layer suggest suppression of nutrient supply to microbes from the surface. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of highly toxic elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

systems biology↗

bioRxiv2017

An interventional Soylent diet increases the Bacteroidetes to Firmicutes ratio in human gut microbiome communities: a randomized controlled trial

Our knowledge of the relationship between the gut microbiome and health has rapidly expanded in recent years. Diet has been shown to have causative effects on microbiome composition, which can have subsequent implications on health. Soylent 2.0 is a liquid meal replacement drink that satisfies nearly 20% of all recommended daily intakes per serving. This study aims to characterize the changes in gut microbiota composition resulting from a short-term Soylent diet. Fourteen participants were separated into two groups: 5 in the regular diet group and 9 in the Soylent diet group. The regular diet group maintained a diet closely resembling self-reported regular diets. The Soylent diet group underwent three dietary phases: A) a regular diet for 2 days, B) a Soylent-only diet (five servings of Soylent daily and water as needed) for 4 days, and C) a regular diet for 4 days. Daily logs self-reporting diet, Bristol stool ratings, and any abdominal discomfort were electronically submitted. Eight fecal samples per participant were collected using fecal sampling kits, which were subsequently sent to uBiome, Inc. for sample processing and V4 16S rDNA sequencing. Reads were clustered into operational taxonomic units (OTUs) and taxonomically identified against the GreenGenes 16S database. We find that an individuals alpha-diversity is not significantly altered during a Soylent-only diet. In addition, principal coordinate analysis using the unweighted UniFrac distance metric shows samples cluster strongly by individual and not by dietary phase. Among Soylent dieters, we find a significant increase in the ratio of Bacteroidetes to Firmicutes abundance, which is associated with several positive health outcomes, including reduced risks of obesity and intestinal inflammation.

clinical trials↗

bioRxiv2017

Evolutionary Insights On The Structure And Function Of Archaeal C/D Box sRNAs As Revealed By A Comprehensive Set From Six Pyrobaculum Species

Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches, and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

molecular biology↗