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The trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.

Objective: An increasing number of patients with significant comorbidities present for complex cardiac surgery, with a subgroup requiring discharge to long-term acute care facilities. We aim to examine predictors and mortality after discharge to a long-term acute care facility., Methods: From January 1, 2015, to April 30, 2021, all adult cardiac surgeries were queried and patients discharged to long-term acute care facilities were identified. Baseline characteristics, procedures, and in-hospital complications were compared between long-term acute care facility and non-long-term acute care facility discharges. Random forest analysis was conducted to establish predictors of discharge to long-term acute care facilities. Kaplan-Meier survival analysis was used to determine probability of survival over 7 years. Multivariate regression modeling was used to establish predictors of death after long-term acute care facility discharge., Results: Of 29,884 patients undergoing cardiac surgery, 324 (1.1%) were discharged to a long-term acute care facility. The long-term acute care facility group had higher rates of urgent/emergency operation (54% vs 23%; 10% vs 3%, P < .001) and longer mean cardiopulmonary bypass (167 vs 110 minutes, P < .001). By random forest analysis, emergency/urgent status, longer cardiopulmonary bypass duration, redo surgery, endocarditis, and history of dialysis were the most predictive of discharge to a long-term acute care facility. Although the non-long-term acute care facility group demonstrated greater than 95% survival at 6 months, Kaplan-Meier survival analysis showed 28% 6-month mortality in the long-term acute care facility cohort. Random forest analysis demonstrated that chronic lung disease and postoperative respiratory complications were significant predictors of death at 6 months after discharge to a long-term acute care facility., Conclusions: Patients with chronic lung and kidney disease undergoing prolonged procedures are at higher risk to be discharged to long-term acute care facilities after surgery with worse survival. Efforts to minimize postoperative respiratory complications may reduce mortality after discharge to long-term acute care facilities., Competing Interests: Conflict of Interest Statement A.M.G. is a consultant for AtriCure, Medtronic, Edwards Lifesciences, Abbott, CryoLife, and ClearFlow. H.E. has a financial relationship with Edwards Lifesciences and LifeNet Health. All other authors reported no conflicts of interest. The Journal policy requires editors and reviewers to disclose conflicts of interest and to decline handling or reviewing manuscripts for which they may have a conflict of interest. The editors and reviewers of this article have no conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduction: The purpose of this study was to report the incidence of iatrogenic sural nerve injury in a large, consecutive sample of surgically managed ankle fractures and to identify factors associated with sural nerve injury and subsequent recovery. We hypothesize that a direct posterior approach may be associated with higher risk of iatrogenic sural nerve injury., Methods: A retrospective cohort study of 265 skeletally mature patients who sustained ankle fractures over a 2-year period was done. All were treated with open reduction and internal fixation of fractured malleoli. Patient, injury, and treatment features were documented. The presence (n = 26, 9.8%) of sural nerve injury and recovery of sural nerve function were noted., Results: All 26 sural nerve injuries were iatrogenic, occurring postoperatively after open reduction and internal fixation. Patients who sustained sural nerve injuries had more ankle fractures secondary to motor vehicle collisions (23.1% versus 9.2%), more associated trimalleolar fractures (69.2% versus 33.9%), and more Orthopaedic Trauma Association/AO 44B3 fractures (57.7% versus 25.1%), all P < 0.05. A posterior approach to the posterior malleolus through the prone position was used in 20.4% of patients. All 26 of the sural nerve injuries (100%) occurred when the patient was placed prone for a posterior approach, P < 0.001. Therefore, 26 of the 54 patients (48%) treated with a posterior approach sustained an iatrogenic sural nerve injury. 62% of patients had full recovery of sural nerve function with no residual numbness, and patients with nerve recovery had fewer associated fracture-dislocations (23.1% versus 100%, P = 0.003)., Conclusions: A posterior approach for posterior malleolus fixation was associated with a 48% iatrogenic sural nerve injury rate, with 62% recovering full function within 6 months of injury. Morbidity of this approach should be considered, and surgeons should be cautious with nerve handling., Level of Evidence: Level III, Therapeutic., (Copyright © 2024 by the American Academy of Orthopaedic Surgeons.)

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought-providing a time series of short-term transcriptional response during rewetting., Competing Interests: The authors declare no conflict of interest.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences., (© 2024. UT-Battelle, LLC, Pacific Northwest National Laboratory and The Author(s).)

Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Calcified right atrial thrombus is rare and commonly occurs secondary to atrial fibrillation and long-term central venous catheterization which present risk for embolization. Treatment typically involves anticoagulation and antiplatelet therapy but rarely surgical excision can be performed, especially in patients with venous obstruction or concomitant valvular dysfunction., Case Presentation: We present the case of a 69 year old symptomatic female with a history of atrial fibrillation and long-term venous catheterization found to have a large calcified right atrial thrombus causing inferior vena cava obstruction and severe tricuspid regurgitation. Patient underwent full median sternotomy with ascending arterial cannulation with superior vena cava and femoral venous cannulation. Intraoperatively, extensive right atrial calcified thrombus was found extending into the inferior vena cava and involving the septal portion of the tricuspid valve annulus causing regurgitation. The calcified thrombus was removed which resolved the inferior vena cava obstruction and the tricuspid valve was repaired by transecting septal leaflet chordae, commissuroplasty, and ring annuloplasty. Postoperative course was uncomplicated and pathology confirmed a calcified right atrial thrombus. At 6 month follow up, the patient was asymptomatic with echocardiogram showing no inferior vena cava stenosis and trivial tricuspid regurgitation., Conclusions: Surgical excision of calcified right atrial thrombus is rare and is often indicated for symptomatic patients with extensive involvement causing venous inflow obstruction or valvular dysfunction. Sufficient preoperative imaging and a multi-disciplinary approach are essential for accurate diagnosis to guide targeted treatment. When the tricuspid valve is involved, repair is preferred over replacement in this patient population given their propensity for calcification and thrombus formation which may result in an increased risk of early bioprosthetic valve degeneration or mechanical valve thrombosis., (© 2024. The Author(s).)

Congenital heart defects (CHDs) are complex conditions affecting the heart and/or great vessels that are present at birth. These defects occur in approximately 9 in every 1000 live births. From diagnosis to intervention, care has dramatically improved over the last several decades. Patients with CHDs are now living well into adulthood. However, there are factors that have been associated with poor outcomes across the lifespan of these patients. These factors include sociodemographic and socioeconomic positions. This commentary examined the disparities and solutions within the evolution of CHD care in the United States.

Introduction Glenohumeral osteoarthritis (GHOA) is a common cause of musculoskeletal pain (MSP) that can frequently lead to pain and functional disability in patients throughout the world. GHOA can be managed with conservative or surgical interventions, although conservative interventions, such as physical therapy (PT), are generally first-line interventions depending on the severity of GHOA. The purpose of this retrospective analysis was to examine how conventional PT impacts outcomes for patients with GHOA based on the severity of radiographic GHOA findings. Methods This study is a retrospective chart review of patients who were referred to PT for MSP and received PT in the outpatient setting between 2016 and 2022. Inclusion criteria were patients who received PT in the outpatient setting, received PT for MSP, had shoulder radiograph imaging within two years of initial PT evaluation, had more than one PT visit (i.e. attended a follow-up session after initial evaluation), and did not have a history of shoulder surgery. Primary outcome measures were pain, abduction active range-of-motion (AROM), and disability via the quick disabilities of the arm, shoulder, and hand (DASH). Patients were divided into the No GHOA group (n=104), Mild GHOA group (n=61), and Moderate/Severe GHOA group (n=55) based on the radiographic GHOA severity. Results All included patients (n=220) had a mean age of 62.2 ± 12.4 years old with a mean number of PT visits of 7.8 ± 4.5 visits. There was initially a significant difference in the magnitude of pain improvement between the three groups based on radiographic severity of GHOA (Kruskal-Wallis H=6.038; p=0.049); however, post hoc testing revealed no significant difference between any of the three groups for pain improvement (p=0.061 to p=1.000). There was also no significant difference in the magnitude of abduction AROM improvement between the three groups based on the radiographic severity of GHOA (Kruskal-Wallis H=2.887; p=0.236). Finally, there was no significant difference in the magnitude of disability improvement via the Quick DASH between the three groups based on the radiographic severity of GHOA (Kruskal-Wallis H=0.156; p=0.925). Conclusion Patients with GHOA referred to PT experience small but statistically significant short-term improvements in pain, abduction AROM, and disability regardless of GHOA radiographic severity. There is no significant association between the magnitude of clinical improvement and the severity of radiographic GHOA. However, despite statistically significant improvements in pain, only patients with mild GHOA experienced clinically significant improvements in pain. Patients with GHOA, regardless of severity, may or may not experience clinically significant improvements in disability after PT., Competing Interests: The authors have declared financial relationships, which are detailed in the next section., (Copyright © 2023, Baumann et al.)

Background: The purpose of this study was to compare clinical, implant-related, and patient-reported outcomes of shoulders undergoing conversion to reverse total shoulder arthroplasty (rTSA) following previous open reduction-internal fixation vs. shoulders undergoing rTSA as a primary treatment modality for acute proximal humeral fractures (PHFs) in patients aged ≥65 years., Methods: We performed a retrospective analysis of a prospectively collected cohort of patients who underwent primary rTSA for PHFs vs. a cohort who underwent conversion arthroplasty with rTSA following fracture repair between 2009 and 2020. Outcomes were assessed preoperatively and at latest follow-up. Demographic characteristics and outcomes were analyzed between cohorts using conventional statistics, as well as stratification by minimal clinically important difference and substantial clinical benefit thresholds where applicable., Results: In total, 406 patients met the study criteria, of whom 322 underwent primary rTSA for PHF and 84 underwent conversion rTSA after failed PHF open reduction-internal fixation. The conversion rTSA cohort was, on average, 7 years younger than the primary rTSA cohort (65 ± 10 years vs. 72 ± 9 years, P < .001). The follow-up periods were similar between the cohorts, with an average of 47.1 months (range, 24-138 months). The percentages of Neer 3-part (41.9% vs. 45.2%) and 4-part (49.1% vs. 46.4%) PHFs were similar (P > .99). The primary rTSA cohort achieved higher forward elevation, external rotation, and patient-reported outcome measurements including Simple Shoulder Test, American Shoulder and Elbow Surgeons, University of California-Los Angeles, Constant, Shoulder Arthroplasty Smart, and Shoulder Pain and Disability Index scores at a minimum of 24 months postoperatively (P < .05 for all). Patient satisfaction was higher in the primary rTSA group than in the conversion rTSA cohort (P = .002). Patient-reported outcome measures uniformly favored the primary rTSA cohort, rising to the level of statistical significance for forward elevation, American Shoulder and Elbow Surgeons score, and Shoulder Pain and Disability Index score (P < .05) relative to substantial clinical benefit. The adverse event rate and revision rate in the conversion rTSA cohort were higher than those in the primary rTSA cohort (26.2% vs. 2.5% [P < .001] and 8.3% vs. 1.6% [P = .001], respectively). At 10 years postoperatively, the revision-free implant survival rate was significantly lower in the conversion cohort compared with the primary cohort (66% vs. 94%, P = .012). Finally, the hazard ratio of revision was 3.69 in the conversion rTSA cohort compared with only 1.0 in the primary rTSA cohort., Conclusion: This study demonstrates that elderly patients who undergo rTSA as a conversion procedure following previous osteosynthesis do not fare as well as those treated with rTSA for acute displaced PHFs. Conversion rTSA patients report lower patient satisfaction and have significantly restricted range of shoulder motion, a higher risk of complications, a higher risk of revision, poorer patient-reported outcomes, and a shorter implant survival rate at 10 years compared with patients undergoing acute rTSA., (Copyright © 2023. Published by Elsevier Inc.)

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans., (© 2023. The Author(s).)

Introduction Musculoskeletal shoulder pain (MSP) is a common condition frequently treated in an outpatient setting by a physical therapy rehabilitation team. Treatment teams can consist of physical therapists (PTs) with or without physical therapist assistants (PTAs). It is currently unknown how different physical therapy team compositions can impact patient outcomes in the outpatient setting. The purpose of this study is to examine how the addition of PTAs to a physical therapy treatment team would impact clinical outcomes when treating patients with MSP in the outpatient setting. Methods This study is a retrospective cohort analysis comparing clinical outcomes for pain, active range of motion (AROM), and disability for patients with MSP when treated by physical therapy treatment teams with or without the presence of PTAs. Inclusion criteria were patients treated for MSP in an outpatient physical therapy clinic without a history of shoulder surgery. Depending on the rehabilitation team composition, patients were divided into a PT-only group or a PTA group. Results Total patients (n = 238) had a mean age of 62.6 ± 12.6 years (median: 64 years) with a mean total number of physical therapy visits of 7.8 ± 4.9 visits (median: 7.0 visits). Of the entire cohort, the PT-only group had 100 patients and the PTA group had 138 patients. There was no significant difference in the magnitude of pain improvement (mean: 1.5 versus 1.9 points, p = 0.177), the magnitude of abduction AROM improvement (mean: 17.6 versus 13.9 degrees, p = 0.173), and the magnitude of disability improvement (mean: 18.9 versus 13.4 percentage points, p = 0.221) between the PT-only group and the PTA group. However, the PT-only group had significantly fewer total visits as compared to the PTA group (6.7 versus 8.6 visits, p < 0.001). Conclusion The addition of PTAs to a rehabilitation team when treating patients with MSP in the outpatient setting does not appear to adversely impact pain, AROM, or disability outcomes. However, patients treated only by PTs had significantly less visits with similar outcomes. More research is needed to determine the interplay between cost, healthcare utilization, and patient outcomes to maximize quality care., Competing Interests: The authors have declared financial relationships, which are detailed in the next section., (Copyright © 2023, Baumann et al.)

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. Video Abstract., (© 2023. The Author(s).)

Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors. Here, we demonstrate that heterologous expression of the REVEILLE1 gene (named AaRVE1) from Agave (Agave americana) not only delays the onset of bud dormancy but also accelerates bud break in poplar in field trials. AaRVE1 heterologous expression increases poplar biomass yield by 166% in the greenhouse. Furthermore, we reveal that heterologous expression of AaRVE1 increases cytokinin contents, represses multiple dormancy-related genes, and up-regulates bud break-related genes, and that AaRVE1 functions as a transcriptional repressor and regulates the activity of the DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) promoter. Our findings demonstrate that AaRVE1 appears to function as a regulator of bud dormancy and bud break, which has important implications for extending the growing season of deciduous trees in frost-free temperate and subtropical regions to increase crop yield., Competing Interests: Conflict of interest statement. Authors declare no conflict of interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops., (© 2022 John Wiley & Sons Ltd.)

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established based on lactate cross-feeding to produce butyrate and butanol from plant biomass. Several co-culture formulations were assembled that consisted of anaerobic fungi (Anaeromyces robustus, Neocallimastix californiae, or Caecomyces churrovis) with the bacterium Clostridium acetobutylicum. Co-cultures were grown simultaneously (e.g., 'one pot'), and compared to cultures where bacteria were cultured in fungal hydrolysate sequentially. Fungal hydrolysis of lignocellulose resulted in 7-11 mM amounts of glucose and xylose, as well as acetate, formate, ethanol, and lactate to support clostridial growth. Under these conditions, one-stage simultaneous co-culture of anaerobic fungi with C. acetobutylicum promoted the production of butyrate up to 30 mM. Alternatively, two-stage growth slightly promoted solventogenesis and elevated butanol levels (∼4-9 mM). Transcriptional regulation in the two-stage growth condition indicated that this cultivation method may decrease the time required to reach solventogenesis and induce the expression of cellulose-degrading genes in C. acetobutylicum due to relieved carbon-catabolite repression. Overall, this study demonstrates a proof of concept for biobutanol and bio-butyrate production from lignocellulose using an anaerobic fungal-bacterial co-culture system., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society of Industrial Microbiology and Biotechnology.)

We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially warmed, and geothermally warmed conditions across Europe. These data will enable further research regarding the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning of northern peatland ecosystems.

Objective: Adaptive laboratory evolution (ALE) is an effective approach to study the evolution behavior of bacterial cultures and to select for strains with desired metabolic features. In this study, we explored the possibility of evolving Thermotoga sp. strain RQ7 for cellulose-degrading abilities., Results: Wild type RQ7 strain was subject to a series of transfers over six and half years with cellulose filter paper as the main and eventually the sole carbon source. Each transfer was accompanied with the addition of 50 μg of Caldicellulosiruptor saccharolyticus DSM 8903 genomic DNA. A total of 331 transfers were completed. No cellulose degradation was observed with the RQ7 cultures. Thirty three (33) isolates from six time points were sampled and sequenced. Nineteen (19) of the 33 isolates were unique, and the rest were duplicated clones. None of the isolates acquired C. saccharolyticus DNA, but all accumulated small-scale mutations throughout their genomes. Sequence analyses revealed 35 mutations that were preserved throughout the generations and another 15 mutations emerged near the end of the study. Many of the affected genes participate in phosphate metabolism, substrate transport, stress response, sensory transduction, and gene regulation., (© 2022. The Author(s).)

The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the "Shed light in The daRk lineagES of the fungal tree of life" (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.

Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans , without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans ., (Copyright © 2020 Bruckbauer, Martin, Minkoff, Veling, Lancaster, Liu, Trimarco, Bushnell, Lipzen, Wood, Sussman, Pennacchio and Cox.)

Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes., (Copyright © 2020 Coleine et al.)

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.

In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that Escherichia coli could acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have now undertaken an extended effort to generate E. coli populations that are as resistant to IR as Deinococcus radiodurans After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent to D. radiodurans Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident. IMPORTANCE Some bacterial species exhibit astonishing resistance to ionizing radiation, with Deinococcus radiodurans being the archetype. As natural IR sources rarely exceed mGy levels, the capacity of Deinococcus to survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains of Escherichia coli with IR resistance levels comparable to Deinococcus Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. However, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent., (Copyright © 2019 American Society for Microbiology.)

By directed evolution in the laboratory, we previously generated populations of Escherichia coli that exhibit a complex new phenotype, extreme resistance to ionizing radiation (IR). The molecular basis of this extremophile phenotype, involving strain isolates with a 3-4 order of magnitude increase in IR resistance at 3000 Gy, is now addressed. Of 69 mutations identified in one of our most highly adapted isolates, functional experiments demonstrate that the IR resistance phenotype is almost entirely accounted for by only three of these nucleotide changes, in the DNA metabolism genes recA, dnaB, and yfjK. Four additional genetic changes make small but measurable contributions. Whereas multiple contributions to IR resistance are evident in this study, our results highlight a particular adaptation mechanism not adequately considered in studies to date: Genetic innovations involving pre-existing DNA repair functions can play a predominant role in the acquisition of an IR resistance phenotype. DOI: http://dx.doi.org/10.7554/eLife.01322.001., Competing Interests: The authors declare that no competing interests exist.

Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5' and 3' ends of 93 312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger-ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi&#95;cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid-monolignol biosynthesis pathway., (© 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.)

The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have been affected by the revised annotation.

Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10-200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) coding-potential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

A diode-pumped Q-switched Nd:YAG laser that operates at the eye-safe 1444 nm wavelength has been developed. When pumped by a 10-W fiber-coupled array at 808 nm, it generated 1 W in cw operation and 560 mW at 20-kHz repetition rate with active Q-switching. Design issues such as thermal lensing characterization and beam quality are discussed.