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At least 199 records · Page 11

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Abstract Background Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗

Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments

Background: The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood. Results: We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34 TS , both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11 T and Phoenicimicrobium oleiphilum HX-OS.bin.34 TS ferment sugars and n-alkanes, respectively, producing H 2 , CO 2 , and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments. Conclusion: Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory.

59 BASIC BIOLOGICAL SCIENCES↗

Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex

The Fusarium sambucinum species complex (FSAMSC) is one of the most taxonomically challenging groups of fusaria, comprising prominent mycotoxigenic plant pathogens and other species with various lifestyles. Among toxins produced by members of the FSAMSC, trichothecenes pose the most significant threat to public health. Herein a global collection of 171 strains, originating from diverse hosts or substrates, were selected to represent FSAMSC diversity. This strain collection was used to assess their species diversity, evaluate their potential to produce trichothecenes, and cause disease on wheat. Maximum likelihood and Bayesian analyses of a combined 3-gene dataset used to infer evolutionary relationships revealed that the 171 strains originally received as 48 species represent 74 genealogically exclusive phylogenetically distinct species distributed among six strongly supported clades: Brachygibbosum, Graminearum, Longipes, Novel, Sambucinum, and Sporotrichioides. Most of the strains produced trichothecenes in vitro but varied in type, indicating that the six clades correspond to type A, type B, or both types of trichothecene-producing lineages. Furthermore, five strains representing two putative novel species within the Sambucinum Clade produced two newly discovered type A trichothecenes, 15-keto NX-2 and 15-keto NX-3. Strains of the two putatively novel species together with members of the Graminearum Clade were aggressive toward wheat when tested for pathogenicity on heads of the susceptible cultivar Apogee. In planta, the Graminearum Clade strains produced nivalenol or deoxynivalenol and the aggressive Sambucinum Clade strains synthesized NX-3 and 15-keto NX-3. Other strains within the Brachygibbosum, Longipes, Novel, Sambucinum, and Sporotrichioides Clades were nonpathogenic or could infect the inoculated floret without spreading within the head. Moreover, most of these strains did not produce any toxin in the inoculated spikelets. These data highlight aggressiveness toward wheat appears to be influenced by the type of toxin produced and that it is not limited to members of the Graminearum Clade.

59 BASIC BIOLOGICAL SCIENCES↗

Riparian vegetation composition and diversity shows resilience following cessation of livestock grazing in northeastern Oregon, USA

Riparian ecosystem restoration has been accomplished through exclusion of livestock using corridor fencing along hundreds of kilometers of streams in the western United States, for the benefit of riparian-obligate wildlife and endangered fishes. Yet, there are limited scientific studies that have evaluated more than short-term shifts in vegetation composition and diversity at a single location or handful of locations following grazing. We sampled riparian vegetation composition along 11-paired grazed and ungrazed (exclosed) stream reaches in northeastern Oregon. Exclosure ages ranged from 2 to >30 years and grazing treatments varied from light grazing every one out of three years to heavy season-long grazing. Species richness and diversity was higher in the ungrazed reaches (p = 0.002). The abundance of native sedges ( Carex spp.) and broad-leaved forbs were also significantly (p ≤ 0.05) greater in ungrazed areas. In contrast, exotic species adapted to grazing such as Poa pratensis and Trifolium repens were more abundant in grazed stream reaches. The prevalence of hydrophytic species significantly increased (p ≤ 0.01) in ungrazed reaches, (based on wetland species indicator scores), indicating that wetland-dominated communities within the ungrazed stream reaches were replacing ones adapted to drier environments. The increased abundance of facultative and wetland-obligate species in ungrazed reaches compared to grazed reaches suggests that livestock grazing exacerbates those climate change effects also leading to warmer and drier conditions. Further, riparian-obligate shrub cover along the streambank was higher in 7 of 8 exclosures that were older than 5 years (p = 0.05). As a restoration approach, the inherent resilience of riparian ecosystems exhibited in ungrazed riparian zones suggest positive feedbacks to other beneficial ecosystem processes such as increased species and habitat diversity, increased carbon sequestration, enhanced allochthonous inputs and greater sediment retention, that would affect the aquatic and terrestrial biota, water quality, and stream morphology.

Kauffman, J. Boone (ORCID:0000000290202815)↗

A fast comparative genome browser for diverse bacteria and archaea

Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast . genomics , that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast . genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast . genomics is available at https://fast.genomics.lbl.gov .

59 BASIC BIOLOGICAL SCIENCES↗

A novel framework for increasing research transparency: Exploring the connection between diversity and innovation

A split sample/dual method research protocol is demonstrated to increase transparency while reducing the probability of false discovery. We apply the protocol to examine whether diversity in ownership teams increases or decreases the likelihood of a firm reporting a novel innovation using data from the 2018 United States Census Bureau’s Annual Business Survey. Transparency is increased in three ways: 1) all specification testing and identifying potentially productive models is done in an exploratory subsample that 2) preserves the validity of hypothesis test statistics fromde novoestimation in the holdout confirmatory sample with 3) all findings publicly documented in an earlier registered report and in this journal publication. Bayesian estimation procedures that leverage information from the exploratory stage included in the confirmatory stage estimation replace traditional frequentist null hypothesis significance testing. In addition to increasing statistical power by using information from the full sample, Bayesian methods directly estimate a probability distribution for the magnitude of an effect, allowing much richer inference. Estimated magnitudes of diversity along academic discipline, race, ethnicity, and foreign-born status dimensions are positively associated with innovation. A maximally diverse ownership team on these dimensions would be roughly six times more likely to report new-to-market innovation than a homophilic team.

Science & Technology - Other Topics↗

Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate

The genus Monosporascus represents an enigmatic group of fungi important in agriculture and widely distributed in natural arid ecosystems. Of the nine described species, two (M. cannonballus and M. eutypoides) are important pathogens on the roots of members of Cucurbitaceae in agricultural settings. The remaining seven species are capable of colonizing roots from a diverse host range without causing obvious disease symptoms. Recent molecular and culture studies have shown that members of the genus are nearly ubiquitous as root endophytes in arid environments of the Southwestern United States. Isolates have been obtained from apparently healthy roots of grasses, shrubs and herbaceous plants located in central New Mexico and other regions of the Southwest. Phylogenetic and genomic analyses reveal substantial diversity in these isolates. The New Mexico isolates include close relatives of M. cannonballus and M. ibericus, as well as isolates that represent previously unrecognized lineages. To explore evolutionary relationships within the genus and gain insights into potential ecological functions, we sequenced and assembled the genomes of three M. cannonballus isolates, one M. ibericus isolate, and six diverse New Mexico isolates. The assembled genomes were significantly larger than what is typical for the Sordariomycetes despite having predicted gene numbers similar to other members of the class. Differences in predicted genome content and organization were observed between endophytic and pathogenic lineages of Monosporascus. Several Monosporascus isolates appear to form associations with members of the bacterial genus Ralstonia (Burkholdariaceae).

59 BASIC BIOLOGICAL SCIENCES↗

Using a 1D Radially Symmetric Coda Envelope Model for Robust Moment Magnitude ( M w ) Estimation in Iraq’s Tectonically Diverse Zones

Robust estimation of moment magnitude (M w ) can be challenging for Iraq due to the strong lateral heterogeneity across diverse tectonic zones. We aim to improve moment magnitude estimation by investigating the reliability of using a 1D coda envelope model in diverse tectonic zones of different lateral effects and offer a way forward for reliable estimates of M w for small events that are difficult to waveform model. Iraq comprises two main tectonic zones: (1) the Outer platform, consisting of the northwestern Zagros fold-thrust belt and the Mesopotamian foredeep, and (2) the Inner Arabian platform which is overlain by the Iraqi desert. A simple 1D coda envelope model was used because coda waves have a low sensitivity to the source and path heterogeneity. Three separate coda calibrations were conducted to investigate the robustness of a single 1D calibration to fit the country: Whole-region calibration, Zagros calibration, and Mesopotamia calibration. In the whole-region calibration, we used stations from both the Zagros and Mesopotamia zones. In the two other calibration models, we used only stations that were in those particular zones. Ground-truth reference spectra derived from the coda spectral ratio method were used to constrain high-frequency site terms. There was no drastic difference when comparing the moment magnitudes calculated from the waveform modeling and the three calibration models. The results show that the 1D coda envelope model is a reliable method even for a region with diverse tectonic zones. Therefore, we recommend using the whole-region calibration model for moment magnitude estimation that provides more complete path coverage and avoids biases introduced by path correction failures. The proposed calibration is a fundamental step in updating the comprehensive earthquake catalog and probabilistic seismic hazard assessments for Iraq.

58 GEOSCIENCES↗

Diversion Path Analysis: A Proposed Methodology to Develop an MC&A Approach for Liquid-Fueled Molten Salt Reactors

Nuclear material control and accounting (MC&A) is a critical element of both the US Nuclear Regulatory Commission (NRC) and US Department of Energy (DOE)’s domestic safeguards and security requirements. NRC licensees are required, under Title 10 of the Code of Federal Regulations (10 CFR) Part 74 to establish and maintain an MC&A program that captures and records the quantities and locations of special nuclear material (SNM) at the facility. Along with physical protection, MC&A is a key element of domestic nuclear material safeguards that enables the NRC to ensure that SNM is controlled and accounted for. SNM, per 10 CFR Part 74, refers to plutonium, 233 U, and uranium enriched in the isotope 233 U or 235 U, but does not include source material. Periodic physical inventories, coupled with material balance evaluations, are effective and demonstrated tools to account for and detect theft or diversion of SNM in facilities containing SNM in bulk material form (i.e., not in discrete, countable items). Historically in the United States, these types of facilities have included fuel fabrication, conversion, and enrichment facilities. In comparison, reactors have relied on item counting of assemblies and control of SNM while in containment (e.g., a sealed reactor pressure vessel) because, to date, reactor fuel has been in item form. In liquid-fueled molten salt reactors (MSRs), unlike traditional light water reactors (LWRs) or bulk facilities, bulk SNM quantities can change significantly during operation as a result of depletion and transmutation. This introduces challenges to the use of traditional periodic physical inventories and material balance evaluations to detect theft or diversion of SNM in reactors that use SNM in bulk material form. Liquid-fueled (i.e., salt-fueled) MSR facilities are MSRs that use SNM within a salt eutectic as the fuel. The SNM is in a bulk material form any time it is outside of fresh or spent fuel storage containers. Some examples of when SNM will be in bulk form in the facility are during addition of fuel to the reactor system, while fuel is circulating in operation, and while fuel is in a drain tank. Periodic physical inventories and material balance evaluations can likely be effectively applied to many portions of an MSR facility, including all areas where depletion and transmutation are not significantly changing the quantities of SNM within the control area. Within an MSR facility, this would include fresh fuel receipt and loading, waste streams that may contain SNM, irradiated fuel storage outside of the reactor core, and any irradiated fuel processing that may happen after SNM has been removed from the reactor. All of these process steps could rely on measurements of SNM quantities compared with documented inventories. Any discrepancies from predicted (i.e., book) inventories and measured inventories could be quantified as inventory differences, consistent with traditional MC&A guidance from the NRC (e.g., in NUREG-1065 Revision 2, NUREG-2159 Revision 1, and RG 5.29 Revision 2). Within the reactor system, additions and removals to the book inventory include depletion of the SNM (e.g., fission of 235 U), which complicates the use of physical inventories. SNM control, however, can also likely be effectively applied to detect theft of SNM throughout a liquid-fueled MSR facility. To complement these approaches, prior technical reports have identified that a diversion path analysis may be a useful, risk-informed, and performance-based tool to determine suitable elements of an MC&A approach for the reactor system within a liquid-fueled MSR facility.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Giant kelp genetic monitoring before and after disturbance reveals stable genetic diversity in Southern California

Given the impacts of climate change and other anthropogenic stressors on marine systems, there is a need to accurately predict how species respond to changing environments and disturbance regimes. The use of genetic tools to monitor temporal trends in populations gives ecologists the ability to estimate changes in genetic diversity and effective population size that may be undetectable by traditional census methods. Although multiple studies have used temporal genetic analysis, they usually involve commercially important species, and rarely sample before and after disturbance. In this study, we run a temporal analysis of giant kelp, Macrocystis pyrifera , genetic diversity over the scope of 10 years (2008-2018) using the same microsatellite marker panel to assess the genetic consequences of disturbance in several populations of giant kelp ( Macrocystis pyrifera ) in the Southern California Bight. The study is a rare pre- and post-disturbance microsatellite analysis that included declines to giant kelp caused by the 2015/16 El Nino Southern Oscillation event. We used canopy biomass estimated by remote sensing (Landsat) to quantify the extent of disturbance to kelp beds, and sea surface temperature data to understand how kelp was pushed towards its temperature limits during this period. Despite prolonged periods with decreased canopy at several sites, no changes in genetic structure and allelic richness were observed. We argue that giant kelp in the region is best described as a “patchy population” system where true extinctions are rare. We discuss how deep refugia of subsurface sporophytes and cryptic microscopic life stages could have kept genetic diversity through disturbance. Given the increasing effects of climate change and uncertainty in modeling impacts of species with cryptic life history stages, we suggest further investigation to reveal the role such stages play in species resilience. Genetic monitoring studies of sites selected by remote census demographic and climate surveys should be continued in the future given the predicted impacts of climate change.

Klingbeil, III, William H.↗

Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes ), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia , Planctomycetes , and Armatimonadetes ). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN.

59 BASIC BIOLOGICAL SCIENCES↗

Impacts of corn intercropping with soybean, peanut and millet through different planting patterns on population dynamics and community diversity of insects under fertilizer reduction

Corn is one of the key grain crops in China and the excessive use of chemical fertilizers and pesticides seriously damages the ecological environment in fields. To explore a more scientific and reasonable way to plant corn and simultaneously reduce the overuse of chemical fertilizers and pesticides, the impact of corn intercropping with soybean, peanut, and millet, respectively, through five planting patterns, including three intercropping patterns (2 corn rows to 2, 3 and 4 rows of soybean/peanut or 2, 4 and 6 millet rows, respectively) and two monoculture patterns of corn and soybean, peanut or millet under normal (600 kg/ha) and reduced (375 kg/ha) levels of NPK (N:P 2 O 5 :K 2 O = 15:15:15) fertilization on the population abundance and community diversity of insects, leaf nutrients, and induced plant hormones jasmonic acid (JA) and salicylic acid (SA) was studied in 2018 and 2019. The results showed that the insect community indexes of the species number ( S ), the diversity index ( H ), and the uniformity index ( E ) generally increased under intercropping and were significantly higher than those under corn monoculture. The prevalence of Asian corn borer ( Ostrinia furnacalis ) on the intercropping corn plants decreased by based on the average of seven surveys per year for each treatment 2.9 to 17 heads per 30 plants compared with that on the monoculture corn plants. The number of natural enemy insect species on corn plants under intercropping was significantly higher than that under corn monoculture. That is, intercropping may decrease the population of Asian corn borers by increasing S , H , E , and natural enemy insect species (NEI). Moreover, intercropping type and fertilizer level significantly affected corn leaf nutrient contents. Compared with the normal fertilizer level, fertilizer reduction significantly reduced the foliar contents of amino acids, soluble protein, and soluble sugar in corn plants. In addition, corn–soybean and corn–peanut intercropping significantly increased the three nutrient contents in corn leaves compared with corn monoculture. In terms of corn nutrients, intercropping could compensate for the effects of fertilizer reduction. The foliar content of JA in corn–soybean intercropping was significantly higher than in corn monoculture. Under corn–soybean and corn–peanut intercropping, SA was significantly lower than under corn monoculture. Overall, intercropping, not fertilizer reduction, can significantly increase insect community diversity while reducing the population abundances of the key insect pest species on corn plants. Intercropping reduced the SA content, increased amino acids and thus reduced the susceptibility of corn to the pest insects.

Li, Likun↗

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗

Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family.

Naviculisporaceae↗

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Bacterial-fungal interactions (BFIs) play an integral role in shaping microbial community composition, biogeochemical functions, spatial dynamics, and microbial dispersal. Mycelial networks created by filamentous fungi or other filamentous microorganisms (e.g., Oomycetes) act as 'fungal highways' that can be utilized by bacteria for transport throughout heterogeneous environments, greatly facilitating their mobility and granting them access to regions that may be challenging or impossible to reach on their own (e.g., due to air pockets within the soil). Several devices and experimental protocols have been created to study these fungal highways, including fungal highway columns. The fungal highway column designed by our group can be used for a variety of in situ or in vitro applications, as well as with diverse environmental and host-associated sample types. Herein, we describe the methods for performing experiments with these columns, including designing, printing, sterilizing, and preparing the devices. The options for analyzing data obtained from the use of these devices are also discussed here, and troubleshooting advice regarding potential pitfalls associated with experiments using fungal highway columns is offered. These devices can be used to gain a more comprehensive understanding of the diversity, mechanisms, and dynamics of fungal highway BFIs to provide valuable insights into the structural and functional dynamics within complex environments (e.g., soils) and across diverse habitats in which bacteria and fungi co-exist.

59 BASIC BIOLOGICAL SCIENCES↗

Galaxy Size and Rotation Curve Diversity in ΛCDM with Baryons

The observed rotation curves of dwarf galaxies exhibit significant diversity at fixed halo mass, challenging galaxy formation within the cold dark matter (CDM) model. Previous cosmological galaxy formation simulations with baryonic physics fail to reproduce the full diversity of rotation curves, suggesting that there is a flaw in baryonic feedback models, observational bias, or that an alternative to CDM must be invoked. In this work, we use the Marvelous Massive Dwarf zoom-in simulations, a suite of high-resolution dwarf simulations with M 200 ∼ 10 10 –10 11 M ⊙ and M * ∼ 10 7 –10 9 M ⊙ , designed to target the mass range where the galaxy rotation curve diversity is maximized, i.e., between and 100 km s −1 . We add to this a set of low-mass galaxies from the Marvel Dwarf Zoom Volumes to extend the galaxy mass range to lower values. Our fiducial star formation and feedback models produce simulated dwarfs with a broader range of rotation curve shapes, similar to observations. These simulations both create dark matter cores via baryonic feedback, reproducing the slower-rising rotation curves, while also allowing for compact galaxies and steeply rising rotation curves. Our simulated dwarfs also reproduce the observed size–M * relation, including scatter, producing both extended and compact dwarfs for the first time in simulated field dwarfs. However, the slowly rising and high baryon mass fraction, as well as the steeply rising and low baryon mass fraction, remain missing. We explore star formation and feedback models and conclude that previous simulations may have had feedback that was too strong to produce compact dwarfs.

Cruz, Akaxia [Flatiron Institute, New York, NY (Un↗

Constraining the particle-scale diversity of black carbon light absorption using a unified framework

Abstract. Atmospheric black carbon (BC), the strongest absorber of visible solar radiation in the atmosphere, manifests across a wide spectrum of morphologies and compositional heterogeneity. Phenomenologically, the distribution of BC among diverse particles of varied composition gives rise to enhancement of its light absorption capabilities by over twofold in comparison to that of nascent or unmixed homogeneous BC. This situation has challenged the modeling community to consider the full complexity and diversity of BC on a per-particle basis for accurate estimation of its light absorption. The conventionally adopted core–shell approximation, although computationally inexpensive, is inadequate not only in estimating but also capturing absorption trends for ambient BC. Here we develop a unified framework that encompasses the complex diversity in BC morphology and composition using a single metric, the phase shift parameter (ρBC), which quantifies how much phase shift the incoming light waves encounter across a particle compared to that in its absence. We systematically investigate variations in ρBC across the multi-space distribution of BC morphology, mixing state, mass, and composition as reported by field and laboratory observations. We find that ρBC>1 leads to decreased absorption by BC, which explains the weaker absorption enhancements observed in certain regional BC compared to laboratory results of similar mixing state. We formulate universal scaling laws centered on ρBC and provide physics-based insights regarding core–shell approximation overestimating BC light absorption. We conclude by packaging our framework in an open-source Python application to facilitate community-level use in future BC-related research. The package has two main functionalities. The first functionality is for forward problems, wherein experimentally measured BC mixing state and assumed BC morphology are input, and the aerosol absorption properties are output. The second functionality is for inverse problems, wherein experimentally measured BC mixing state and absorption are input, and the morphology of BC is returned. Further, if absorption is measured at multiple wavelengths, the package facilitates the estimation of the imaginary refractive index of coating materials by combining the forward and inverse procedures. Our framework thus provides a computationally inexpensive source for calculation of absorption by BC and can be used to constrain light absorption throughout the atmospheric lifetime of BC.

54 ENVIRONMENTAL SCIENCES↗