Beginning the Journey: Disability Inclusion Pledge Survey Findings and Recommendations

The Disability & Philanthropy Forum is an emerging philanthropy-serving organization created by the Presidents' Council on Disability Inclusion in Philanthropy. Central to the Forum's mission is expanding philanthropic commitment to disability rights and justice by centering the leadership of the disability community.To help funders and philanthropy-serving organizations as they engage in their disability inclusion journeys, the Forum created the Disability Inclusion Pledge. The Pledge identifies concrete ways for funders and others in the sector to actively shift away from policies and practices that perpetuate ableism — the systemic stigmatization of and discrimination against people with disabilities — and uplift disability as an essential component of advancing equity.Beginning the Journey: Disability Inclusion Pledge Survey Findings and Recommendations provides a baseline measurement of how current practices and plans of responding Pledge signatories align with each of the eight action agendas included in the Pledge

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Mars Aquarius Mission and Titan Explorer

The Mars Aquarius Mission is designed to carry out several scientific studies of the surface and subsurface of Mars with an emphasis on locating subterranean water. This mission is a precursor to a manned mission to Mars. A manned mission will require an extended stay on the planet's surface, and an accessible source of water will greatly simplify life support requirements. Using data from previous Mars observations, four sites were selected as possible locations of subsurface water. The Aquarius spacecraft carries one penetrator for each of these sites

Global marine bacterial diversity peaks at high latitudes in winter.

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms

Marked seasonal variation in the wild mouse gut microbiota

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations

Existing climate change will lead to pronounced shifts in the diversity of soil prokaryotes

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 3 (2018): e00167-18, doi:10.1128/mSystems.00167-18.Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.This work was supported by the Strategic Priority Research Program (XDB15010101, XDA05050404) of the Chinese Academy of Sciences, the National Program on Key Basic Research Project (2014CB954002, 2014CB954004), the National Natural Science Foundation of China (41701298, 41371254), the “135” Plan and Frontiers Projects of Institute of Soil Science (ISSASIP1641), and the National Science and Technology Foundation project (2015FY110100). J.A.G. was supported by the U.S. Dept. of Energy under contract DE-AC02-06CH11357. N.F. was supported by a grant from the National Science Foundation (DEB-0953331). K.S.P. and J.L. were supported by the National Science Foundation (DMS-1069303), the Gordon and Betty Moore Foundation (grant no. 3300), the Gladstone Institutes, and a gift from the San Simeon Fund

Toward a global platform for linking soil biodiversity data

Soil biodiversity is immense, with an estimated 10–100 million organisms belonging to over 5000 taxa in a handful of soil. In spite of the importance of soil biodiversity for ecosystem functions and services, information on soil species, from taxonomy to biogeographical patterns, is incomplete and there is no infrastructure to connect pre-existing or future data. Here, we propose a global platform to allow for greater access to soil biodiversity information by linking databases and repositories through a single open portal. The proposed platform would for the first time, link data on soil organisms from different global sites and biomes, and will be inclusive of all data types, from molecular sequences to morphology measurements and other supporting information. Access to soil biodiversity species records and information will be instrumental to progressing scientific research and education. Further, as demonstrated by previous biodiversity synthesis efforts, data availability is key for adapting to, and creating mitigation plans in response to global changes. With the rapid influx of soil biodiversity data, now is the time to take the first steps forward in establishing a global soil biodiversity information platform

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Microbial communities feature an immense diversity of species and this diversity is linked with outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, diversity depends on the amount of nutrient supplied due to an "early-bird" effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.Comment: Appendix follows main tex

Global ecotypes in the ubiquitous marine clade SAR86

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world’s oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades

Towards a global platform for linking soil biodiversity data

Soil biodiversity is immense, with an estimated 10–100 million organisms belonging to over 5000 taxa in a handful of soil. In spite of the importance of soil biodiversity for ecosystem functions and services, information on soil species, from taxonomy to biogeographical patterns, is incomplete and there is no infrastructure to connect pre-existing or future data. Here, we propose a global platform to allow for greater access to soil biodiversity information by linking databases and repositories through a single open portal. The proposed platform would for the first time, link data on soil organisms from different global sites and biomes, and will be inclusive of all data types, from molecular sequences to morphology measurements and other supporting information. Access to soil biodiversity species records and information will be instrumental to progressing scientific research and education. Further, as demonstrated by previous biodiversity synthesis efforts, data availability is key for adapting to, and creating mitigation plans in response to global changes. With the rapid influx of soil biodiversity data, now is the time to take the first steps forward in establishing a global soil biodiversity information platform