Biology subjects

Sieradzki, E. T.

Publications and source records attributed to Sieradzki, E. T..

18 recordsLinked to original sources

bioRxiv2025

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland

Changes in global patterns can leave a lasting legacy in semi-arid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn--a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O, and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux; measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing; and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by [~]1 order of magnitude, yielding decreased community growth efficiency (CGE = gross community growth/net respiration), and microbial mortality declined by [~]2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover), this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low-CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting. Persistent decreases in CGE due to reduced winter rainfall result in consistent carbon loss as CO2, which, if sustained over multiple years, could ultimately lead to a net decline in total soil organic carbon.

microbiology↗

bioRxiv2024

Phosphate amendment drives bloom of RNA viruses after soil wet-up

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting--while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2,190 RNA viral populations were identified across five phyla, with 37% of these predicted to infect bacteria (26%) or fungi (11%). Only 1.2% of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages, particularly Leviviricetes, proliferated significantly. Notably, 60% of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 107-109 bacteria per gram of soil, aligning with the total bacterial population (107-1010 g-1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect. HighlightsO_LISoil wet-up influences RNA virus dynamics for over a week C_LIO_LIThe majority of hosts predicted for RNA viruses were bacteria and fungi C_LIO_LIPhosphate amendment preferentially supports Lenarviricota over other RNA viruses C_LIO_LI60% of vOTUs that responded to phosphate were from unknown bacteriophage clades C_LIO_LIMost soil bacteria are predicted to be infected by RNA bacteriophages within a week C_LI

microbiology↗

bioRxiv2024

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period greatly impacts soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils--however this is often through measurements in culture. Here, we used metagenome-assembled genomes in combination with metatranscriptomics and 18O- water stable isotope probing to track genomic traits associated with transcriptional activity and growth of soil microorganisms over the course of one week following rewetting of a grassland soil. We found that the codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also observed higher growth rates in bacteria with smaller genomes, demonstrating that reduced genome size contributes to bacterial growth responses to sudden changes in water or nutrient availability--potentially explaining why smaller genomes are more prevalent in arid and carbon poor systems. High levels of codon bias corresponded to faster transcriptional upregulation of ribosomal protein genes. In early transcribing taxa, nucleotides requiring less energy to produce were more common at synonymous substitution sites--where nucleotide substitutions did not change the encoded amino acid. We found several of these relationships also existed within a phylum, suggesting that association between genomic traits and activity could be a generalized characteristic of soil bacteria. These results provide in situ evidence that following rewetting, certain genomic characteristics affect soil microbial growth rate and transcription, and points towards the fitness advantages that these traits might pose for bacteria under changing conditions in soil.

microbiology↗

bioRxiv2024

Vitamin B12 variants structure soil microbial communities despite soil's vast reservoir of B12.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

microbiology↗

bioRxiv2023

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

Interactions between plant roots and rhizosphere bacteria mediate nitrogen (N)-cycling processes and create habitats rich in low molecular weight (growing roots, rhizosphere) and complex organic molecules (decaying root litter, detritusphere) compared to bulk soil. Microbial N-cycling is regulated by a diverse suite of genes from many interconnected metabolic pathways; but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat and time. Here we present an analysis of a replicated time series of soil metatranscriptomes; we followed multiple N transformations in four soil habitats (rhizosphere, detritusphere, mixed rhizo-/detriusphere, bulk soil) over a period of active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectory of N-cycling gene expression. Across soil habitats, the most highly expressed N-transformation genes were related to extracellular proteases, ammonium assimilation into microbial biomass via glutamate synthase, and ammonium oxidation. Upregulation of bacterial assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, bacterial ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of ammonium oxidation genes was almost exclusively performed by three phylotypes of Thaumarchaeota and was upregulated in unamended bulk soil. Unidirectional ammonium assimilation and its regulatory genes (glutamine synthetase/glutamate synthase, or GS/GOGAT) were upregulated in soil surrounding relatively young roots and more highly decayed root litter, suggesting N may have been limiting in these habitats (the GS/GOGAT pathway is known to be activated under low N availability). We did not detect expression of N-fixation or anammox genes. Our comprehensive metatranscriptomic time-series of organic and inorganic N-cycling in rhizosphere, detritusphere, and bulk soil, indicates that differences in C and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil microhabitats that exist in close spatial proximity. Contribution to the fieldPlant roots modulate microbial nitrogen cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots (rhizosphere), decaying roots (detritusphere), near both (rhizo/detritusphere), or outside the direct influence of roots (bulk). While many genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in the primary four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involving in multiple nitrogen pathways. We also found populations with genes for multiple pathways, where expression was likely shaped by available forms of carbon and by competition with plants for inorganic nitrogen. Phylogenetic differences in spatial and temporal expression of the soil microbial N-pathway genes ultimately regulate N-availability to plants.

ecology↗

bioRxiv2022

Isotope-enrichment reveals active viruses follow microbial host dynamics during rewetting of a California grassland soil

Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigated lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicated that dry soil held a diverse but low biomass reservoir of virions, of which only a subset thrived following wet-up. Viral richness decreased by 50% within 24 h post wet-up, while viral biomass increased four-fold within one week. Counter to recent hypotheses suggesting temperate viruses predominate in soil, our evidence indicates that wet-up is dominated by viruses in lytic cycles. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.

microbiology↗

bioRxiv2022

Viruses of soil ammonia oxidising archaea identified using a novel DNA stable isotope probing approach for low GC mol% genomes

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived 13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of 13C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in 13C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.

microbiology↗

bioRxiv2022

Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history

Rewetting of seasonally dry soils induces a burst of microbial activity and carbon mineralization that changes nutrient availability and leads to succession. Yet the microbial functions that underpin this succession are not well described. Further, its unclear how previous precipitation frames microbial capacities after rewetting and how long these effects persist. We used isotopically-labeled water to rewet seasonally dry annual grassland soil that experienced either mean annual or reduced precipitation during the previous two years, and sampled at five subsequent time points. We used quantitative stable isotope probing (qSIP)-informed genome- resolved metagenomics to identify growing microorganisms, predict their capabilities, and analyze how these traits differed over time and between precipitation treatments. Organisms that grew after wetup were more abundant than non-growing organisms prior to the wet-up, suggesting that traits that initiate succession are pre-defined at the end of the prior plant growing season or via survival over the summer. Fast-growing organisms had fewer carbohydrate active enzyme (CAZy) genes per genome than slower-growing organisms, suggesting that although fast-growers were capable of degrading complex C, they may not specialize in this process. Differential abundance of CAZy genes in growing organisms throughout the succession implies that substrate availability varied with time. In contrast, the abundance of peptidases in growing organisms differed between precipitation treatments, but not over time following wet-up. Before wet-up, the soil organisms gene inventories were different between the two precipitation treatments. Surprisingly, this legacy effect waned after just one week. Thus, pre-wetup differences in microbial functional capacity converged shortly after rewetting.

microbiology↗

bioRxiv2022

Substantial differences in soil viral community composition within and among four Northern California habitats

Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral dynamics are poorly understood, particularly in soil. Here, we identified trends in soil viral community composition in relation to habitat, moisture content, and physical distance. We generated 30 soil viromes from four distinct habitats (wetlands, grasslands, woodlands, and chaparral) by selectively capturing virus-sized particles prior to DNA extraction, and we recovered 3,432 unique viral species (vOTUs). Viral communities differed significantly by soil moisture content, with viral richness generally higher in wet compared to dry soil habitats. However, vOTUs were rarely shared between samples, including replicates <10 m apart, suggesting that soil viruses may not disperse well and that future soil viral community sampling strategies may need to account for extreme community differences over small spatial scales. Of the 19% of vOTUs detected in more than one sample, 93% were from the same habitat and site, suggesting greater viral community similarity in closer proximity and under similar environmental conditions. Within-habitat differences indicate that extensive sampling would be required for rigorous cross-habitat comparisons, and results belie emerging paradigms of higher viral activity in wet soils and soil viral community spatial heterogeneity.

microbiology↗

bioRxiv2022

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are likely dependent on current and prior soil moisture levels. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) to an H218O labeling experiment to determine which microbial community members, and with what capacities, are growing under in situ conditions. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve an active subset of soil community members and identify the ecophysiological traits that characterize them. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to bacteria that were heavily isotopically labeled, we identified abundant isotope-labeled phages suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capabilities to decompose the diverse complex carbohydrates common in soil necromass or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation.

microbiology↗

bioRxiv2021

Edaphic controls on genome size and GC content of bacteria in soil microbial communities

Bacteria in soil microbial communities are crucial to terrestrial ecosystem function, yet our understanding of the fundamental characteristics of their genomes, such as GC content and genome size, is not complete. Much of our understanding of the mechanisms which shape their genomic traits is derived from other systems or from isolated bacteria. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine which environmental parameters most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, especially soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil C:N, indicating potential resource driven selection against AT base pairs. As soil bacteria tend to be more carbon limited, smaller genomes with higher GC content may reduce the cost of reproduction in carbon-limited soils. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin nucleotide and amino acid selection in soil bacterial communities.

ecology↗

bioRxiv2021

The Functional Significance of Bacterial Predators

Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to non-predatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than non-predatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolfpack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than non-predators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from non-predators. This finding supports ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow, and that predatory bacteria influence element flow through microbial food webs.

ecology↗

bioRxiv2020

Methane-derived carbon flow through host-virus trophic networks in soil

The concentration of atmospheric methane continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of organisms regulating methane production and consumption, the frequency and impact of interactions with viruses on their activity in soil is unknown. Metagenomic sequencing of soil microbial communities has enabled identification of linkages between viruses and hosts. However, determining host-virus linkages through sequencing does not determine whether a virus or a host are active. In this study, we identified active individual interactions in situ by following the transfer of assimilated carbon from active hosts to viruses. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized methane-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilisers of carbon, together with the recent transfer of methane-derived carbon to viruses. Sixty-three percent of viral contigs from replicated soil incubations contained genes associated with known methanotrophic bacteria. Genomic sequences from 13C-enriched viruses were present in clustered regularly interspaced short palindromic repeats (CRISPR) arrays of multiple, closely-related Methylocystis populations, revealing differences in their history of viral interaction. Viruses infecting non-methanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with methane-fueled microbial food networks.

microbiology↗

bioRxiv2020

Transcription of protease and chitinase genes provides a window onto macromolecular organic nitrogen decomposition in soil

Nitrogen (N) commonly limits terrestrial plant growth partly because most soil-N is present as macromolecular organic compounds and not directly available to plants. Soil microbes degrade these large N-containing substrates to gradually release plant-available inorganic-N throughout the growing season, potentially meeting plant demand. Knowing which microbes are responsible for release of organic N, as well as their spatiotemporal patterns of activity, can enable microbial management strategies that increase plant access to soil-N and reduce dependency on fertilizer-N. We used time-resolved metatranscriptomes to follow taxonomy-resolved differential expression of N-depolymerizing enzymes. Taxonomic groups show adaptations based on extracellular proteases to specialized habitats in soil characterized by presence (Betaproteobacteria) or absence (Thaumarcheota) of live roots and root detritus (Deltaproteobacteria and Fungi). A similar increase of eukaryotic chitinases near root detritus hints at predation of fungi. Others demonstrate temporal patterns such as increasing expression over time, implying increased competitiveness with substrate depletion (Chloroflexi). Phylotypes from the same genus can have different potential benefits to the plant based on protease expression (e.g., Janthinobacterium), which should be considered when designing bioaugmentation. We identify one Janthinobacterium phylotype and two Burkholderiales that may be candidates for bioaugmentation near young roots and a Rhizobacter which could benefit mature roots.

microbiology↗

bioRxiv2020

Metagenomics and quantitative stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We demonstrate the ability of a local seed community of degraders at the Port of LA to incorporate carbon from naphthalene, leading to a quick shift in the microbial community composition to be dominated by these normally rare taxa. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes and even when combining genes from the entire microbial community. We analyze metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate metagenomic-based recommendations for future optimization of PAHs bioremediation. ImportanceOil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil, and have a significant role in degradation of oil spills. The most recalcitrant and toxic component of oil is polycyclic aromatic hydrocarbons. Therefore, the bacteria who can break those molecules down are of particular importance. We identified such bacteria at the port of Los Angeles, one of the busiest ports worldwide, and characterized their metabolic capabilities. Based on those analyses we proposed chemical targets to stimulate the activity of these bacteria in case of an oil spill in the port of LA.

microbiology↗

bioRxiv2020

Measurement error and resolution in quantitative stable isotope probing: implications for experimental design

Quantitative stable isotope probing (qSIP) estimates the degree of incorporation of an isotope tracer into nucleic acids of metabolically active organisms and can be applied to microorganisms growing in complex communities, such as the microbiomes of soil or water. As such, qSIP has the potential to link microbial biodiversity and biogeochemistry. As with any technique involving quantitative estimation, qSIP involves measurement error; a more complete understanding of error, precision and statistical power will aid in the design of qSIP experiments and interpretation of qSIP data. We used several existing qSIP datasets of microbial communities found in soil and water to evaluate how variance in the estimate of isotope incorporation depends on organism abundance and on the resolution of the density fractionation scheme. We also assessed statistical power for replicated qSIP studies, and sensitivity and specificity for unreplicated designs. We found that variance declines as taxon abundance increases. Increasing the number of density fractions reduces variance, although the benefit of added fractions declines as the number of fractions increases. Specifically, nine fractions appear to be a reasonable tradeoff between cost and precision for most qSIP applications. Increasing replication improves power and reduces the minimum detectable threshold for inferring isotope uptake to 5 atom%. Finally, we provide evidence for the importance of internal standards to calibrate the %GC to mean weighted density regression per sample. These results should benefit those designing future SIP experiments, and provide a reference for metagenomic SIP applications where financial and computational limitations constrain experimental scope. ImportanceOne of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about genomic content and potential functions, but may not reflect an organisms activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions, but fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and function of specific microbes within a naturally occurring community. Here we explore how the resolution of density-gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional replication, and cost-benefit balanced scenarios for SIP experimental design.

microbiology↗

bioRxiv2019

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

microbiology↗

bioRxiv2017

Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metatranscriptomes

Viruses are an important top-down control on microbial communities, yet their direct study in natural environments has been hindered by culture limitations1-3. The advance of sequencing and bioinformatics over the last decade enabled the cultivation independent study of viruses. Many studies focus on assembling new viral genomes4-6 and studying viral diversity using marker genes amplified from free viruses7,8. We used cellular metatranscriptomics to study community-wide viral infections at three coastal California sites throughout a year. Generation of and recruitment to viral contigs (> 5kbp, N=66) allowed tracking of infection dynamics over time and space. Here we show that while these assemblies represent viral populations, they are likely biased towards clonal or low diversity assemblages. Furthermore, we demonstrate that published T4-like cyanophages (N=50) and pelagiphages (N=4), having genomic continuity between close relatives, are better tracked using marker genes. Additionally, we demonstrate determination of potential hosts by matching infection dynamics with microbial community composition. Finally, we quantify the relative contribution of various cyanobacteria and viruses to photosystem-II psbA expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression we observed is of viral origin, which highlights the proportion of infected cells and makes viruses a remarkable contributor to photosynthesis and oxygen production.

ecology↗