Nutrient (C, N and P) enrichment induces significant changes in the soil metabolite profile and microbial carbon partitioning

The cycling of soil organic matter (SOM) and carbon (C) within the soil is governed by the presence of key macronutrients, particularly nitrogen (N) and phosphorus (P). The relative ratio of these nutrients has a direct effect on the potential rates of microbial growth and nutrient processing in soil and thus is fundamental to ecosystem functioning. However, the effect of changing soil nutrient stoichiometry on the small organic molecule (i.e., metabolite) composition and cycling by the microbial community remains poorly understood. Here, we aimed to disentangle the effect of stoichiometrically balanced nutrient addition on the soil metabolomic profile and apparent microbial carbon use efficiency (CUE) by adding a labile C source (glucose) in combination with N and/or P. After incorporation of the added glucose into the microbial biomass (48 h), metabolite profiling was undertaken by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). 494 metabolites were identified across all treatments mainly consisting of lipids (n = 199), amino acids (n = 118) and carbohydrates (n = 43), >97% of which showed significant changes in concentration between at least one treatment. Overall, glucose-C addition generally increased the synthesis of other carbohydrates in soil, while addition of C and N together increased peptide synthesis, indicative of protein formation and turnover. The combination of C and P significantly increased the number of fatty acids synthesised. There was no significant change in the PLFA-derived microbial community structure or microbial biomass following C, N and P addition. Further, N addition led to an increase in glucose-C partitioning into anabolic processes (i.e., increased CUE), suggesting the microbial community was N, but not P limited. Based on the metabolomic profiles observed here, we conclude that inorganic nutrient enrichment causes substantial shifts in both primary and secondary metabolism within the microbial community, leading to changes in resource flow and thus soil functioning, however, the microbial community illustrated significant metabolic flexibility

SARS-CoV-2 Mitigation Strategies, Testing, and Cases at 254 Jails in the US Southeast, October 2020 to May 2021

Objectives. To characterize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mitigation strategies, testing, and cases across county jails in the Southeastern United States, examining variability by jail characteristics. Methods. We administered a 1-time telephone survey to personnel of 254 jails in Alabama, Georgia, North Carolina, and South Carolina between October 2020 and May 2021. Results. Some SARS-CoV-2 mitigation strategies (e.g., screening at intake, isolation and masking for symptomatic persons) were commonly reported (≥ 75% of jails). Other measures, such as masking regardless of symptoms (52%) and screening at release (26%), were less common and varied by jail state or population size. Overall, 41% of jails reported no SARS-CoV-2 testing in the past 30 days. Jails with testing (59%) tested a median of 6 per 100 incarcerated persons; of those jails, one third reported 1 or more cases of positive tests. Although most jails detected no cases, in the 20% of all jails with 1 or more case in the past 30 days, 1 in 5 tests was positive. Conclusions. There was low testing coverage and variable implementation of SARS-CoV-2 mitigation strategies in Southeastern US jails during the first year of the COVID-19 pandemic

Medicaid Enrollment among Prison Inmates in a Non-expansion State: Exploring Predisposing, Enabling, and Need Factors Related to Enrollment Pre-incarceration and Post-Release

Prison inmates suffer from a heavy burden of physical and mental health problems and have considerable need for healthcare and coverage after prison release. The Affordable Care Act may have increased Medicaid access for some of those who need coverage in Medicaid expansion states, but inmates in non-expansion states still have high need for Medicaid coverage and face unique barriers to enrollment. We sought to explore barriers and facilitators to Medicaid enrollment among prison inmates in a non-expansion state. We conducted qualitative interviews with 20 recently hospitalized male prison inmates who had been approached by a prison social worker due to probable Medicaid eligibility, as determined by the inmates’ financial status, health, and past Medicaid enrollment. Interviews were transcribed verbatim and analyzed using a codebook with both thematic and interpretive codes. Coded interview text was then analyzed to identify predisposing, enabling, and need factors related to participants’ Medicaid enrollment prior to prison and intentions to enroll after release. Study participants’ median age, years incarcerated at the time of the interview, and projected remaining sentence length were 50, 4, and 2 years, respectively. Participants were categorized into three sub-groups based on their self-reported experience with Medicaid_ (1) those who never applied for Medicaid before prison (n = 6); (2) those who unsuccessfully attempted to enroll in Medicaid before prison (n = 3); and (3) those who enrolled in Medicaid before prison (n = 11). The six participants who had never applied to Medicaid before their incarceration did not hold strong attitudes about Medicaid and mostly had little need for Medicaid due to being generally healthy or having coverage available from other sources such as the Veteran’s Administration. However, one inmate who had never applied for Medicaid struggled considerably to access mental healthcare due to lapses in employer-based health coverage and attributed his incarceration to this unmet need for treatment. Three inmates with high medical need had their Medicaid applications rejected at least once pre-incarceration, resulting in periods without health coverage that led to worsening health and financial hardship for two of them. Eleven inmates with high medical need enrolled in Medicaid without difficulty prior to their incarceration, largely due to enabling factors in the form of assistance with the application by their local Department of Social Services or Social Security Administration, their mothers, medical providers, or prison personnel during a prior incarceration. Nearly all inmates acknowledged that they would need health coverage after release from prison, and more than half reported that they would need to enroll in Medicaid to gain healthcare coverage following their release. Although more population-based assessments are necessary, our findings suggest that greater assistance with Medicaid enrollment may be a key factor so that people in the criminal justice system who qualify for Medicaid—and other social safety net programs—may gain their rightful access to these benefits. Such access may benefit not only the individuals themselves but also the communities to which they return

Can You Hear us Now? Voices from the Margin: Using Indigenous Methodologies in Geographic Research

Indigenous methodologies are an alternative way of thinking about research processes. Although these methodologies vary according to the ways in which different Indigenous communities express their own unique knowledge systems, they do have common traits. This article argues that research on Indigenous issues should be carried out in a manner which is respectful and ethically sound from an Indigenous perspective. This naturally challenges Western research paradigms, yet it also affords opportunities to contribute to the body of knowledge about Indigenous peoples. It is further argued that providing a mechanism for Indigenous peoples to participate in and direct these research agendas ensures that their communal needs are met, and that geographers then learn how to build ethical research relationships with them. Indigenous methodologies do not privilege Indigenous researchers because of their Indigeneity, since there are many ‘insider’ views, and these are thus suitable for both Indigenous and non-Indigenous researchers. However, there is a difference between research done within an Indigenous context using Western methodologies and research done using Indig- enous methodologies which integrates Indigenous voices. This paper will discuss those differences while presenting a historical context of research on Indigenous peoples, providing further insights into what Indigenous methodologies entail, and proposing ways in which the academy can create space for this discourse

Distribution, diversity and environmental adaptation of highland papaya (Vasconcellea spp.) in tropical and subtropical America

Vasconcellea species, often referred to as highland papayas, consist of a group of fruit species that are closely related to the common papaya (Carica papaya). The genus deserves special attention as a number of species show potential as raw material in the tropical fruit industry, fresh or in processed products, or as genetic resources in papaya breeding programs. Some species show a very restricted distribution and are included in the IUCN Red List. This study on Vasconcellea distribution and diversity compiled collection data from five Vasconcellea projects and retrieved data from 62 herbaria, resulting in a total of 1,553 georeferenced collection sites, in 16 countries, including all 21 currently known Vasconcellea species. Spatial analysis of species richness clearly shows that Ecuador, Colombia and Peru are areas of high Vasconcellea diversity. Combination of species occurrence data with climatic data delimitates the potential distribution of each species and allows the modeling of potential richness at continent level. Based on these modeled richness maps, Ecuador appears to be the country with the highest potential Vasconcellea diversity. Despite differences in sampling densities, its neighboring countries, Peru and Colombia, possess high modeled species richness as well. A combination of observed richness maps and modeled potential richness maps makes it possible to identify important collection gaps. A Principal Component Analysis (PCA) of climate data at the collection sites allows us to define climatic preferences and adaptability of the different Vasconcellea species and to compare them with those of the common papaya

Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood Bayesian and parsimony analyses

Copyright © 2007 The Natural history MuseumThe phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second-most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine-erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.Michael S. Y. Lee, Andrew F. Hugall, Robin Lawson & John D. Scanlo

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe