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Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete,

Shifts in generations from Millennials to Generation Z have brought changes to today's classroom. In turn, these changes indicate the need for reform and innovation in education. If the goal for education remains to put contributing members into society, then educators must search for the most effective ways to prepare students to enter society today, rather than in the past. The purpose of this article is to introduce creative ways to share the lives and work of outstanding ecologists to enhance students' knowledge in both English language arts and science, while also addressing state and national standards. Integrating the lives and work of well-known ecologists or environmentalists into middle school science has the potential to enhance the understanding our students have of what it means to be a scientist. Taking these small steps to broaden students' understanding of science and scientists may inspire a young person to consider a science career for themselves someday. The nation and the state have done their parts in giving teachers the outline for student learning and success in science. Now, it is up to teachers to utilize the standards within their classrooms to make science come to life.

BackgroundLinking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.ResultsOur HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.ConclusionsOur semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

Science literacy is at the nation's forefront, and the Next Generation Science Standards were revamped with the goal of guiding teachers in an enhanced approach to science teaching and learning [...]

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Background and Purpose: Individuals post traumatic brain injury (TBI) are likely to experience cognitive, sensory, and motor impairments. Tremor is a common movement disorder that can affect this patient population. The purpose of this case report was to describe the effects that progressive muscle relaxation, meditation, and mental practice-based interventions have on the treatment of chronic right upper extremity tremor in a patient post-TBI. Case Description: A 47-year-old male with a traumatic brain injury presented with a resting and postural tremor of the right wrist flexors and deficits in cognition, sensation, proprioception, balance, and motor function. The patient's primary goal for therapy was to decrease the tremor to improve his quality of life and ability to perform activities of daily living. Methods: Progressive muscle relaxation, breath-focused meditation, and mental practice-based intervention were administered to the patient. Active range of motion activities occurred during weekly in-person sessions and daily practice occurred at home. Results: The patient demonstrated improvements in quality of life, self-ratings of tremor severity, ratings of tremor impact on ADL's, gross motor object manipulation, frequency of tremor via surface electromyography, and visual inspection of a spirograph. Conclusion: A combination of progressive muscle relaxation, meditation, and mental practice-based interventions appeared to positively impact tremor across physical and psychosocial domains in a patient with a chronic tremor. Further investigation is needed to verify these findings. [ABSTRACT FROM AUTHOR]

Oscillating redox conditions are a common feature of humid tropical forest soils, driven by an ample supply and dynamics of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. However, the net result of variable soil redox regimes on iron (Fe) mineral dynamics and associated carbon (C) forms and fluxes is poorly understood in tropical soils. Using a 44-day redox incubation experiment with humid tropical forest soils from Puerto Rico, we examined patterns in Fe and C transformations under four redox regimes: static anoxic, "flux 4-day" (4d oxic, 4d anoxic), "flux 8-day" (8d oxic, 4d anoxic) and static oxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides, and led to an increase in soluble Fe(II) and amorphous Fe oxide pools. Preferential dissolution of the less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic C, presumably due to acidification or direct release of organic matter (OM) from dissolving Fe(III) mineral phases. The average nominal oxidation state of water-soluble C was lowest under persistent anoxic conditions, suggesting that more reduced organic compounds were metabolically unavailable for microbial consumption under reducing conditions. Anoxic soil compounds had high H/C values (and were similar to lignin-like compounds) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic C was highest in static oxic soils. These results show how Fe minerals and Fe-OM interactions in tropical soils are highly sensitive to variable redox effects. Shifting soil oxygen availability rapidly impacted exchanges between mineral-sorbed and aqueous C pools, increased the dissolved organic C pool under anoxic conditions implying that the periodicity of low-redox events may control the fate of C in wet tropical soils.

This article describes a semester-long project developed by the authors to create a positive connection between children and nature. The project integrated reading instruction with science activities to emphasize the natural world in the lives of children. This intervention involved the authors visiting an elementary classroom five times over the course of a semester to teach nature and reading activities. Each lesson consisted of a literary component wherein students read and discussed a single issue of "Keeping Texas Wild," a Texas Parks and Wildlife magazine for children. The purpose of these lessons was to emphasize activities that would necessitate student observation of animals indigenous to the area where the students currently reside. Focusing on such animals increased the probability that students might encounter the wildlife during random outdoor experiences, thus increasing their interest in nature.

Ocular adnexal sebaceous carcinoma (SebCA) represents one of the most clinically problematic periocular tumors, often requiring aggressive surgical resection. The pathobiology of this tumor remains poorly understood, and few models exist that are suitable for preclinical testing. The aim of this study was to establish new cell lines to serve as models for pathobiological and drug testing. With patient consent, freshly resected tumor tissue was cultured using conditional reprogramming cell conditions. Standard techniques were used to characterize the cell lines in terms of overall growth, clonogenicity, apoptosis, and differentiation in vitro. Additional analyses including Western blotting, short tandem repeat (STR) profiling, and next-generation sequencing (NGS) were performed. Drug screening using mitomycin-C (MMC), 5-fluorouricil (5-FU), and 6-Diazo-5-oxo-L-norleucine (DON) were performed. JHH-SebCA01, JHH-SebCA02, and JHH-SebCA03 cell lines were established from two women and one man undergoing surgical resection of eyelid tumors. At passage 15, they each showed a doubling time of two to three days, and all could form colonies in anchorage-dependent conditions, but not in soft agar. The cells contained cytoplasmic vacuoles consistent with sebaceous differentiation, and adipophilin protein was present in all three lines. STR profiling confirmed that all lines were derived from their respective patients. NGS of the primary tumors and their matched cell lines identified numerous shared mutations, including alterations similar to those previously described in SebCA. Treatment with MMC or 5-FU resulted in dose-dependent growth inhibition and the induction of both apoptosis and differentiation. MYC protein was abundant in all three lines, and the glutamine metabolism inhibitor DON, previously shown to target high MYC tumors, slowed the growth of all our SebCA models. Ocular adnexal SebCA cell lines can be established using conditional reprogramming cell conditions, and our three new models are useful for testing therapies and interrogating the functional role of MYC and other possible molecular drivers. Current topical chemotherapies promote both apoptosis and differentiation in SebCA cells, and these tumors appear sensitive to inhibition or MYC-associated metabolic changes. [ABSTRACT FROM AUTHOR]