The extent and ecological significance of intraspecific diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (Rhode Island, USA) phytoplankton community thermal selection experiment. Despite all 11 isolates being highly similar (with average nucleotide identities of >99.9%, with 98.6-100% of the genome aligning), thermal performance curves revealed selection at warm and cool temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Within the fine-scale genetic diversity that did exist within this population, the two divergent thermal ecotypes differed at a locus containing genes for the phycobilisome antenna complex. Our study demonstrates that present-day marine microbial populations can contain microdiversity in the form of cryptic but environmentally-relevant thermotypes that may increase their resilience to future rising temperatures. SignificanceNumerous studies exist comparing the responses of distinct taxonomic groups of marine microbes to a warming ocean (interspecific thermal diversity). For example, Synechococcus, a nearly globally distributed unicellular marine picocyanobacterium that makes significant contributions to oceanic primary productivity, contains numerous taxonomically distinct lineages with well documented temperature relationships. Little is known though about the diversity of functional responses to temperature within a given population where genetic similarity is high (intraspecific thermal diversity). This study suggests that understanding the extent of this functional intraspecific microdiversity is an essential prerequisite to predicting the resilience of biogeochemically essential microbial groups such as marine Synechococcus to a changing climate.

Populating the exoplanet mass-radius diagram in order to identify the underlying relationship that governs planet composition is driving an interdisciplinary effort within the exoplanet community. The discovery of hot super-Earths-a high-temperature, short-period subset of the super-Earth planet population-has presented many unresolved questions concerning the formation, evolution, and composition of rocky planets. We report the discovery of a transiting, ultra-short-period hot super-Earth orbiting TOI-1075 (TIC 351601843), a nearby (d = 61.4 pc) late-K/early-M-dwarf star, using data from the Transiting Exoplanet Survey Satellite. The newly discovered planet has a radius of 1.791(-0.081)(+0.116) R-circle plus and an orbital period of 0.605 day (14.5 hr). We precisely measure the planet mass to be 9.95(-1.30) (+1.36) M-circle plus using radial velocity measurements obtained with the Planet Finder Spectrograph mounted on the Magellan II telescope. Our radial velocity data also show a long-term trend, suggesting an additional planet in the system. While TOI-1075 b is expected to have a substantial H/He atmosphere given its size relative to the radius gap, its high density ( 9.32(-1.85)(+2.05) g cm(-3)) is likely inconsistent with this possibility. We explore TOI-1075 b's location relative to the M-dwarf radius valley, evaluate the planet's prospects for atmospheric characterization, and discuss potential planet formation mechanisms. Studying the TOI -1075 system in the broader context of ultra-short-period planetary systems is necessary for testing planet formation and evolution theories and density-enhancing mechanisms and for future atmospheric and surface characterization studies via emission spectroscopy with the JWST.

Invasive species science has focused heavily on the invasive agent. However, management to protect native species also requires a proactive approach focused on resident communities and the features affecting their vulnerability to invasion impacts. Vulnerability is likely the result of factors acting across spatial scales, from local to regional, and it is the combined effects of these factors that will determine the magnitude of vulnerability. Here, we introduce an analytical framework that quantifies the scale-dependent impact of biological invasions on native richness from the shape of the native species-area relationship (SAR). We leveraged newly available, biogeographically extensive vegetation data from the U.S. National Ecological Observatory Network to assess plant community vulnerability to invasion impact as a function of factors acting across scales. We analyzed more than 1000 SARs widely distributed across the USA along environmental gradients and under different levels of non-native plant cover. Decreases in native richness were consistently associated with non-native species cover, but native richness was compromised only at relatively high levels of non-native cover. After accounting for variation in baseline ecosystem diversity, net primary productivity, and human modification, ecoregions that were colder and wetter were most vulnerable to losses of native plant species at the local level, while warmer and wetter areas were most susceptible at the landscape level. We also document how the combined effects of cross-scale factors result in a heterogeneous spatial pattern of vulnerability. This pattern could not be predicted by analyses at any single scale, underscoring the importance of accounting for factors acting across scales. Simultaneously assessing differences in vulnerability between distinct plant communities at local, landscape, and regional scales provided outputs that can be used to inform policy and management aimed at reducing vulnerability to the impact of plant invasions.

The identification of bright quasars at z greater than or similar to 6 enables detailed studies of supermassive black holes, massive galaxies, structure formation, and the state of the intergalactic medium within the first billion years after the Big Bang. We present the spectroscopic confirmation of 55 quasars at redshifts 5.6 < z < 6.5 and UV magnitudes -24.5 < M (1450) < -28.5 identified in the optical Pan-STARRS1 and near-IR VIKING surveys (48 and 7, respectively). Five of these quasars have independently been discovered in other studies. The quasar sample shows an extensive range of physical properties, including 17 objects with weak emission lines, 10 broad absorption line quasars, and 5 objects with strong radio emission (radio-loud quasars). There are also a few notable sources in the sample, including a blazar candidate at z = 6.23, a likely gravitationally lensed quasar at z = 6.41, and a z = 5.84 quasar in the outskirts of the nearby (D similar to 3 Mpc) spiral galaxy M81. The blazar candidate remains undetected in NOEMA observations of the [C ii] and underlying emission, implying a star formation rate M (circle dot) yr(-1). A significant fraction of the quasars presented here lies at the foundation of the first measurement of the z similar to 6 quasar luminosity function from Pan-STARRS1 (introduced in a companion paper). These quasars will enable further studies of the high-redshift quasar population with current and future facilities.

The application of an external pressure on Metal Halide Perovskite (MHPs) has become a fascinating way of tuning their optical properties, achieving also novel features. Here, the pressure response of 2D MHPs including a long alkyl chain made of ten carbon atoms, namely decylammonium (DA), has been investigated as a function of the central atom in DA2PbI4 and DA2GeI4. The two systems share a common trend in the phase stability, displaying a transition from an orthorhombic to a monoclinic phase around 2 GPa, followed by a phase separation in two monoclinic phases characterized by different c-axis. The optical properties show rather different behavior due to the presence of Pb or Ge. DA2PbI4 shows a progressive red shift of the band gap from 2.28 eV at ambient conditions, to 1.64 eV at 11.5 GPa, with a narrow PL emission composed by two components, with the second one appearing in concomitance with the phase separation and significantly shifted to lower energy. On the other hand, DA2GeI4, changes from a non-PL system at ambient pressure, to a clear broadband emitter centered around 730 nm (FWHM ~ 170 nm), with a large stoke shift, and an intensity maximum at about 3.7 GPa. This work sheds light on the structural stability of 2D perovskites characterized by extended alkyl chains, to date limited to four carbon atoms, and shows the pressure-induced emergence of broad emission in a novel lead-free perovskite, DA2GeI4. The evidence of wide emission by a moderate pressure in a germanium-based 2D MHP represents a novel result which may open the design, by chemical pressure, of efficient wide or even white lead-free emitters.

The computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods used to infer sub-compartments from Hi-C data fail to address the cell population heterogeneity. Here we describe a model-based method, called CscoreTool-M, which uses probabilistic modeling to build multiple 3D genome sub-compartments from Hi-C data. The compartment scores inferred using CscoreTool-M directly represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring local sub-compartment containing heterochromatin marked by Histone lysine trimethylation (H3K27me3) surrounded by the actively transcribed euchromatic regions. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations for different genomic regions. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can further identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions.

In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that lamin C but not the other lamin isoforms rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The immunoglobulinlike fold domain and the NLS were required for the recruitment from the nucleoplasm to the rupture sites with the Barrier-to-autointegration factor (BAF). The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP (cGAMP) synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF and cGAS concertedly accumulate at sites of NE rupture for repair.

A large fraction of heterochromatin in the metazoan genome is associated with the nuclear lamina (NL) in interphase nuclei. This heterochromatin is often referred to as Lamina-Associated Domains (LADs) and are often mapped from cell populations asynchronously progressing through the cell cycle. We and others have recently reported that LADs are largely stable during G1, S, or G2 phases of the cell cycle, and appear similar to LADs mapped from bulk cell populations. LADs in senescent cells, however, are reported to be quite different from proliferating cells, and it remains unclear how senescent cell LADs are established. As cells finish mitosis and re-enter G1, reassembly of the nuclear envelope and NL appears to precede mitotic chromosome decondensation. Therefore, the initial NL interactions with the decondensing chromatin may be quite different from those reported in asynchronous or FACS isolated G1, S, or G2 populations. By developing a modified version of the Tyramide-Signal Amplification sequencing (TSA-seq), which we call chromatin pull down-based Tyramide Signal Amplification-sequencing (cTSA-seq), we uncover a dynamic NL-chromatin interaction as cells progress through G1. The appearance of stable LADs coincides with sufficient chromatin decondensation and active gene expression in G1. Interestingly, early G1 NL-chromatin interactions, which are found toward the telomeric ends of human chromosomes, are similar to those found in oncogene-induced senescent cells. We find that the assembly of LADs during the formation of the G1 nucleus is gradual and that the arrest of NL-chromatin interactions in early G1 may contribute to genome disorganization of senescence cells.

The nuclear lamina (NL) is a proteinaceous network found beneath the inner nuclear membrane. The NL is linked to a number of dynamic cellular activities including chromatin organization, transcription and RNA/protein trafficking through nuclear pores. Our understanding of the NL has been hindered in part by the general insolubility and low extractability of proteins from this region. This has spurred the development of proximity ligation methods that label proteins and/or DNA near the NL for systematic identification (Bar et al., 2018; Chen et al., 2018b; Guelen et al., 2008; Roux et al., 2012). To simplify labeling and improve temporal resolution, we fused APEX2 (Hung et al., 2014; Lam et al., 2015) to the nuclear lamina protein lamin-B1 to map proteins, RNA and DNA associated with the NL. We show that APEX2 labeling of the NL is robust and requires as little as 20 seconds. In addition to identifying the NL proteome, this method revealed NL-proximal RNA species that were largely spliced. These NL-proximal RNAs show a bias toward long 3 UTRs, suggesting an RNA-regulatory role of the NL. This is further supported by the finding of a bias toward longer 3 UTRs in genes deregulated in lamin-null cells. Interestingly, these RNAs share a sequence motif in their 3 UTRs. Finally, we demonstrate that the APEX2 method can reliably map lamina-associated domains (LADs) at different stages of the cell cycle, revealing a variability of short LADs regions enriched for histone lysine 27 trimethylation (H3K27me3). Thus the APEX2 method report here is a useful addition to the molecular toolbox for the study of the NL and permits the identification of proteome, transcriptome, and genome elements associated with this nuclear substructure.

Many hard and soft corals harbor algae for photosynthesis. The algae live inside coral cells in a specialized membrane compartment called symbiosome, which shares the photosynthetically fixed carbon with coral host cells, while host cells provide inorganic carbon for photosynthesis1. This endosymbiotic relationship is critical for corals, but increased environmental stresses are causing corals to expel their endosymbiotic algae, i.e. coral bleaching, leading to coral death and degradation of marine ecosystem2. To date, the molecular pathways that orchestrate algal recognition, uptake, and maintenance in coral cells remain poorly understood. We report chromosome-level genome assembly of a fast-growing soft coral, Xenia species (sp.)3, and its use as a model to decipher the coral-algae endosymbiosis. Single cell RNA-sequencing (scRNA-seq) identified 13 cell types, including gastrodermis and cnidocytes, in Xenia sp. Importantly, we identified the endosymbiotic cell type that expresses a unique set of genes implicated in the recognition, phagocytosis/endocytosis, maintenance of algae, and host coral cell immune modulation. By applying scRNA-seq to investigate algal uptake in our new Xenia sp.. regeneration model, we uncovered a dynamic lineage progression from endosymbiotic progenitor state to mature endosymbiotic and post-endosymbiotic cell states. The evolutionarily conserved genes associated with the endosymbiotic process reported herein open the door to decipher common principles by which different corals uptake and expel their endosymbionts. Our study demonstrates the potential of single cell analyses to examine the similarities and differences of the endosymbiotic lifestyle among different coral species.