Biology subjects

Song, M. J.

Publications and source records attributed to Song, M. J..

16 recordsLinked to original sources

bioRxiv2026

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

Previous studies have shown that there may be more species of Azolla in California than currently recognized, including a recent introduction of the non-native Azolla caroliniana. To better assess the status and species diversity of Azolla in California, we sequenced four historical herbarium specimens, some over 100 years old, and increased our sampling of extant populations across seven counties in California. We found that many specimens from California thought to be Azolla microphylla are actually Azolla filiculoides or members of one of two non-native "Azolla caroliniana" clades. We also found that some specimens collected from California from the 1960s through the 1980s fall within an Azolla microphylla-mexicana clade. However, there is no evidence of this species from any recent collections even from counties where it was previously found, which points to a potential extirpation of this species from California.

ecology↗

bioRxiv2026

Epiphytic cryptogam communities differ little despite strong variation in coastal fog exposure

Because mosses and lichens obtain water directly from their surroundings, coastal fog is expected to strongly influence epiphytic cryptogam communities during the long summer droughts of Mediterranean-climate ecosystems. We examined epiphytic mosses and lichens on coyote brush (Baccharis pilularis) across coastal and inland transects on San Bruno Mountain, California, where marine-layer exposure produces a sharp local microclimate gradient. We surveyed coyote brush availability, sampled standardized branches, monitored temperature and relative humidity, and quantified cryptogam occurrence, diversity, morphology, and reproduction. Morphological and chemical identifications were supplemented with molecular markers, while bacterial 16S sequencing was used to characterize cryptogam-associated microbiomes across host taxa and, for the dominant moss Pulvigera pringlei, across transects. Coastal microsites were cooler and more humid, whereas inland microsites experienced substantially greater daytime atmospheric drying demand. Despite this pronounced environmental contrast, cryptogam abundance, reproduction, and visible community composition differed little between transects, although branch-level genus diversity was modestly higher on the coastal transect. Macrolichen lobe or branch length and cryptogam patch area were greater inland in pooled comparisons, but these differences weakened after accounting for taxonomic composition. Bacterial communities differed strongly among cryptogam host taxa, but the P. pringlei microbiome showed no detectable difference in diversity or composition between coastal and inland transects. The broad similarity of cryptogam communities across a strong fog gradient is consistent with buffering of epiphytic cryptogams against fine-scale variation in marine-layer exposure. For the predominantly green-algal lichens in this community, the ability to absorb water vapor from humid air may reduce dependence on direct fog wetting, while host-associated bacterial communities may be structured more strongly by host identity than by local microclimate. Together, our results show that epiphytic cryptogam communities and microbiomes can remain remarkably similar across pronounced microclimatic variation despite modest morphological shifts.

plant biology↗

bioRxiv2026

An overlooked microbial pathway links organic nitrogen turnover in composts to nitrous oxide formation

Biological N2O production from organic nitrogen is generally assumed to require canonical nitrification, which generates oxidized nitrogen that subsequently fuel denitrification. Whether this paradigm universally applies to nitrogen-rich microbial communities remains unclear. Here, we investigated N2O production across an industrial poultry manure composting process and found that substantial N2O formation occurred despite the apparent absence of canonical ammonia oxidation. Neither allylthiourea inhibition nor metagenomic analyses provided evidence for ammonia-oxidizing microorganisms or their activity. Instead, metagenomic analyses identified abundant bacterial nitric oxide synthase (bNos) genes, many of which were phylogenetically affiliated with Bacilli, the dominant bacterial group throughout composting. Physiological experiments with Bacillus isolates demonstrated a nitrification-independent route in which L-arginine was oxidized to NO2-/NO3-, consistent with bNOS-mediated NO formation followed by abiotic oxidation. Recovery of 15N-labelled N2O following 15NO2- addition established NO2- as an immediate precursor of aerobically produced N2O, confirming that the oxidized nitrogen generated through this alternative route subsequently fueled denitrification. Metagenomic analyses further revealed extensive denitrification potential but comparatively low nosZ abundance. Together, these findings identify a previously overlooked route linking organic nitrogen turnover to denitrification independently of canonical nitrification, thereby expanding current models of microbial N2O production in composts and potentially other protein-rich thermophilic environments.

microbiology↗

bioRxiv2025

Landscape genomics and demography of California Azolla

Azolla was collected and sequenced across California as a part of the California Conservation Genomics Project. We identify three major populations of Azolla in the state. Out of these groups, we are able to confidently identify one as Azolla filiculoides. The other two taxa are seemingly newly reported to California and are not the same as the taxa currently treated by the Jepson Manual; specifically, they are not members of the A. microphylla/mexicana clade. We infer patterns of Azolla genetic diversity across the state and the demographic histories of these populations. We find evidence that both isolation by distance and isolation by environment contribute to spatial genetic variation. Both of the two newly reported populations have demographic histories consistent with recent invasions of the state. However, we also discuss alternative possibilities and propose a roadmap for resolving the taxonomy of California Azolla.

ecology↗

bioRxiv2025

The microbiome of Calasterella californica is shaped mostly by the genetics of the host thalli

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremise of studyC_ST_ABSThe recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility, and the development of new pipelines and databases enable the use short reads to study bacterial communities associated with organisms. MethodsWe utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space. Key resultsThe bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well known plant symbionts. While diversity metrics of bacteria composition was similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality. ConclusionsOur results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. Our novel off-target metagenomics approach can be applied to any population level re-sequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using re-purposed data from landscape genomics.

microbiology↗

bioRxiv2024

The genome assembly of the duckweed fern, Azolla caroliniana

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only two species are currently recognized but there may be up to six putative species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies. The assembly is 521 Mb in length, with a contig N50 of 1.6 Mb, and is scaffolded into 22 pseudo-chromosomes. The BUSCO completeness score is 87.5%, making it the most complete and most contiguous Azolla assembly to date. In combination with the previously published A. filiculoides genome, this A. caroliniana genome will be a powerful tool for understanding the population genetics and taxonomy of one of the most cryptic, economically important, and poorly circumscribed fern taxa, and for facilitating land plant genomics more broadly.

genomics↗

bioRxiv2024

The nitrogen-fixing fern Azolla has a complex microbiome characterized by multiple modes of transmission

Azolla is a floating fern that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont--Anabaena azollae--that performs nitrogen fixation in specialized Azolla leaf pockets. This cyanobac-terium has a greatly reduced genome and appears to be in the "advanced" stages of symbiosis, potentially evolving into a nitrogen-fixing organelle. However, there are also other lesser-known inhabitants of the leaf pocket whose role and mode of transmission are unknown. We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes in order to identify the common bacterial endosymbionts of the leaf pocket and assess their patterns of co-diversification. Four taxa were found across all samples, establishing that there are multiple endosymbionts that consistently inhabit the Azolla leaf pocket. We found varying degrees of co-diversification across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which implies that the endosymbiotic community is transmitted by a mix of horizontal and vertical mechanisms, and that some members of the microbiome are more facultative symbionts than others. These results show that the Azolla symbiotic community is complex, featuring members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

ecology↗

bioRxiv2024

Selective enrichment of Methylococcaceae versus Methylocystaceae methanotrophs via control of methane feeding scheme

Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, how different groups of methanotrophs contribute to this important role in different environmental settings remain ambiguous. Here, in a simplified laboratory setting of well-mixed batch reactors fed continuous flow of CH4-containing gas, methanotrophic microbiomes were enriched from paddy soils under six different incubation conditions prepared as combinations of two different CH4 mixing ratios (0.5% and 10% v/v) and three supplemented Cu2+ concentrations (0, 2, and 10 M). Monitoring of the temporal community shifts in the reactor microbiomes observed domination of Methylocystis spp. in all three reactors fed 0.5% v/v, as further supported by the analyses of pmoCAB genes in the shotgun metagenomes of the single-point samples from the same reactors. Copper deficiency did not select for mmoXYZ-possessing methanotrophs. Instead, a cluster of mbn genes with an abundance accounting for approximately 5% of Methylocystis population was identified, suggesting a comparative ecological importance of methanobactin in Cu-deficient methanotrophy over soluble methane monooxygenases. These findings highlight the importance of Methylocystis spp. in mitigating emissions from CH4 hotspots, e.g., landfills and rice paddies, and suggest the feasibility of directed enrichment/isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production. SynopsisThis study reports enrichment of a complex soil microbiota with 0.5% methane resulting in dominance of a specific group of methane-consuming bacteria Methylocystis, highlighting their ecological significance as CH4 sink.

microbiology↗

bioRxiv2023

Synovial macrophage diversity and activation of M-CSF signaling in post-traumatic osteoarthritis

ObjectiveSynovium is home to immune and stromal cell types that orchestrate inflammation following a joint injury; in particular, macrophages are central protagonists in this process. We sought to define the cellular and temporal dynamics of the synovial immune niche in a mouse model of post-traumatic osteoarthritis (PTOA), and to identify stromal-immune crosstalk mechanisms that coordinate macrophage function and phenotype. DesignWe induced PTOA in mice using a non-invasive tibial compression model of anterior cruciate ligament rupture (ACLR). Single cell RNA-seq and flow cytometry were used to assess immune cell populations in healthy (Sham) and injured (7d and 28d post-ACLR) synovium. Characterization of synovial macrophage polarization states was performed, alongside computational modeling of macrophage differentiation, as well as implicated transcriptional regulators and stromal-immune communication axes. ResultsImmune cell types are broadly represented in healthy synovium, but experience drastic expansion and speciation in PTOA, most notably in the macrophage portion. We identified several polarization states of macrophages in synovium following joint injury, underpinned by distinct transcriptomic signatures, and regulated in part by stromal-derived macrophage colony-stimulating factor signaling. The transcription factors Pu.1, Cebp, Cebp{beta}, and Jun were predicted to control differentiation of systemically derived monocytes into pro-inflammatory synovial macrophages. ConclusionsWe defined different synovial macrophage subpopulations present in healthy and injured mouse synovium. Nuanced characterization of the distinct functions, origins, and disease kinetics of macrophage subtypes in PTOA will be critical for targeting these highly versatile cells for therapeutic purposes.

immunology↗

bioRxiv2023

Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods is hotly debated. Here we test whether five Bayesian methods--Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the cladogenetic diversification rate shift model (CLaDS2)--produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diver-sification rates is strongly method-dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system. Lay SummaryUnderstanding why some groups of organisms have more species than others is key to understanding the origin of biodiversity. Theory and empirical evidence suggest that multiple distinct historical events--such as the evolution of particular morphological features (e.g., the flower, the tetrapod limb) and competition amongst species--can produce this pattern of divergent species richness. Identifying when and where on the tree of life shifts in diversification rates occur is important for explaining the origin of modern-day biodiversity and understanding how disparity among species evolves. Several statistical methods have been developed to infer diversification rates and identify these shifts. While these methods each attempt to make inferences about changes in the tempo of diversification, they differ in their underlying statistical models and assumptions. Here we test if these methods draw similar conclusions using a dataset of 65 time-calibrated phylogenies from across multicellular life. We find that inferences of where rate shifts occur strongly depends on the chosen method. Therefore, biologists should choose the model whose assumptions they believe to be the most valid and justify their model choice a priori, or consider using several independent methods to test an evolutionary hypothesis.

evolutionary biology↗

bioRxiv2021

Induction of autotetraploidy and microbiome associations mediate differential responses to pathogens

It has become increasingly clear that the microbiome plays a critical role in shaping the host organisms response to disease. There also exists mounting evidence that an organisms ploidy level is important in their response to pathogens and parasites. However, no study has determined if or how these two factors influence one another. We investigate the effect of whole-genome duplication in Arabidopsis thaliana on their above-ground (phyllosphere) microbiome, and determine the interacting impacts of ploidy and the microbiome on disease outcome. Using seven independently derived synthetic auto-tetraploid Arabidopsis accessions, a synthetic leaf-associated bacterial community, and the model pathogen Pseudomonas syringae pv. Tomato DC3000, we confirm that polyploids are generally more resistant to pathogens, but illustrate that this resistance may be in part due to a decrease in the reliance on beneficial bacteria. Polyploids fare better against the pathogen than diploids regardless of microbial inoculation, while we observed that diploids harboring an intact microbiome have lower pathogen densities than those without. We then use RNA sequencing to show that diploids have many more differentially expressed defense-related genes in the presence of their phyllosphere microbiota, while polyploids exhibit constitutively activated defenses regardless of exposure to the synthetic community. These results imply that whole-genome duplication can disrupt historical host-microbiome associations, and suggest that a potential cause or consequence of disruption is a heightened capacity for pathogen defense that is less impacted by the microbiome.

plant biology↗

bioRxiv2020

An Analysis of SARS-CoV-2 Using ViReport

The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of cases and hundreds of thousands of deaths. Given the current lack of treatments or vaccines available, it may be useful to trace the evolu-tion and spread of the virus to better develop methods of preventative intervention. In this study, we analyzed over 4,000 full genome sequences of human SARS-CoV-2 using novel tool ViReport [13], an automated workflow for performing phylogenetic analyses on viral sequences and generating comprehensive molecular epidemiologi-cal reports. The complete ViReport output can be found at https://github.com/mirandajsong/ViReport-SARS-CoV-2.

bioinformatics↗

bioRxiv2019

Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana

The Gene Balance Hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage, and that the way in which gene product abundance is governed by gene dosage is consistent for all genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and gene dosage responses immediately following ploidy change. We demonstrate that overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and that individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage-sensitive gene groups (GO terms, metabolic networks, gene families, and predicted interacting protein pairs) exhibit both smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication. This supports the hypothesis that duplicate gene retention patterns are shaped by selection to preserve dosage balance.

plant biology↗

bioRxiv2019

Development of group-specific nosZ quantification method targeting active nitrous oxide reducing population in complex environmental samples

Substantial N2O emission results from activated sludge nitrogen removal processes. The importance of N2O-reducers possessing NosZ-type N2O reductases have been recognized as the only N2O sink in situ key to determination of the net N2O emissions; however, reliable quantification methods for nosZ genes and transcripts have yet to be developed. Here, nosZ genes and transcripts in activated sludge tank microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approach. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primer/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated by comparison with the shotgun metagenome analysis results. With the validated qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.

microbiology↗

bioRxiv2018

Enhanced nitrous oxide production in denitrifying Dechloromonas aromatica strain RCB under salt and alkaline conditions

Salinity and pH are important environmental parameters with direct and indirect impacts on the viability and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N2O accumulated transiently only in insignificant amounts at low salinity ([≤]0.5% NaCl) and circumneutral pH (7.0 and 7.5). Incubation at 0.7% salinity resulted in substantially longer lag phase and slower growth rate, along with the increase in the amounts of transiently accumulated N2O (15.8{+/-}2.8 moles N2O-N/vessel). Incubation at pH 8.0 severely inhibited growth and resulted in permanent accumulation of 29.9{+/-}1.3 moles N2O-N/vessel from reduction of 151{+/-}20 moles NO3-. The transcription analyses observed decreased nosZ/(nirS1+nirS2) ratios coinciding with N2O accumulation. The N2O consumption rates of resting D. aromatica cells subjected to the salt and alkaline stress conditions were significantly lower than the rates of N2O production from NO2- reduction at N2O / NO2- concentration of 0.1 mM, but not at a higher concentration (1.0 mM). These results indicate that alteration in N2O consumption kinetics was another cause of enhanced N2O production observed under the stress conditions. The findings in this study suggest that canonical denitrifiers may become a significant N2O source when faced with abrupt environmental changes.

microbiology↗

bioRxiv2016

PRDX6 inhibits neurogenesis of neural precursor cells through downregulation of wdfy1 mediated TLR4 signal

Impaired neurogenesis has been associated with brain disorders. The role of peroxiredoxin 6 (PRDX6) in the neurodegenerative diseases is very controversial. To demonstrate the role of PRDX6 in neurogenesis, we compared neurogenesis ability and studied the molecular mechanisms. It was found that the neurogenesis of neural stem cells and expression of the marker protein were lowered in PRDX6 Tg-mice compared with non-tg mice. Moreover, the expression of wdfy1 was dramatically decreased in PRDX6-Tg mice, also, we observed that wdfy1 siRNA decreases the differentiation ability of primary neural stem cells to astrocyte and neuronal cells as well as PC12 cells. However, knockdown of PRDX6 recovered neurogenesis in the brain of PRDX6-Tg mice as well as PC-12 cells. We also showed that TLR4 was dramatically reduced in PRDX6 Tg mice as well as PC-12 cells and PRDX6 overexpression reduced neurogenesis was rescued after treatment of TLR4 siRNA. We further found that reduced TLR4 expression and neurogenesis was reversed in the neuron from PRDX6-Tg mice as well as PC12 cells by introduction of wdfy1 plasmid. Moreover, TLR4 siRNA reduced neurogenesis and wdfy1 expression. This study indicated that PRDX6 inhibits neurogenesis of neural precursor cells through TLR4 dependent downregulation of wdfy1.

developmental biology↗