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Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

Boreal forests represent the world's largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth's greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.

The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.

Aim The differential responses of plant species to climate change are of great interest and grave concern for scientists and conservationists. One underexploited resource for better understanding these changes are the records held by herbaria. Using these records to assess the responses of different groups of species across the entire flora of California, we sought to quantify the magnitude of species elevational shifts, to measure differences in shifts among functional groups and between native and introduced species, and to evaluate whether these shifts were related to the conservation of thermal niches. Location California. Methods To characterize these shifts in California, we used 681,609 georeferenced herbarium records to estimate mean shifts in elevational and climatic space of 4426 plant taxa. We developed and employed a statistical method to robustly analyse the data represented in these records. Results We found that 15% of all taxa in California have ranges that have shifted upward over the past century. There are significant differences between range shifts of taxa with different naturalization statuses: 12% of endemic taxa show significant upward range shifts, while a greater proportion (27%) of introduced taxa have shifted upward. We found significant differences between the proportion of significant range shifts across taxa with different seed sizes, but did not find evidence for differences in shift based on life-form (annual versus perennial, herbaceous versus woody). Main conclusions Our analyses suggest that introduced species have disproportionately expanded their ranges upward in elevation over the past century when compared with native species. While these shifts in introduced species may not be exclusively driven by climate, they highlight the importance of considering the interacting factors of climate-driven range shifts and invasion to understand how floras are responding in the face of anthropogenic change.

Fungal endophytes are diverse and widespread symbionts that occur in the living tissues of all lineages of plants without causing evidence of disease. Culture-based and culture-free studies indicate that they often are abundant in the leaves of woody angiosperms, but only a few studies have visualized endophytic fungi in leaf tissues, and the process through which most endophytes colonize leaves has not been studied thoroughly. We inoculated leaf discs and the living leaves of a model woody angiosperm, Populus trichocarpa, which has endophytes that represent three distantly-related genera (Cladosporium, Penicillium, and Trichoderma). We used scanning electron microscopy and light microscopy to evaluate the timeline and processes by which they colonize leaf tissue. Under laboratory conditions with high humidity, conidia germinated on leaf discs to yield hyphae that grew epiphytically and incidentally entered stomata, but did not grow in a directed fashion toward stomatal openings. No cuticular penetration was observed. The endophytes readily colonized the interiors of leaf discs that were detached from living leaves, and could be visualized within discs with light microscopy. Although they were difficult to visualize within the interior of living leaves following in vivo inoculations, standard methods for isolating foliar endophytes confirmed their presence.

The postdoctoral research phase is intended to allow researchers to further develop and strengthen skills needed to succeed in an academic career (NAS et al. 2000). For example, doctoral programs train students to conduct research and publish papers, but often do not include opportunities to develop professional skills, such as project management, balancing multiple research projects, applying for large grants, managing research teams, teaching, and developing the mentorship skills necessary for future careers both within and outside of academia. Many postdoctoral positions, however, do allow early-career researchers to practice these skills sets while deepening their research skills and expanding their collaboration network. Thus, job candidates that have postdoctoral experience are often viewed as more competitive in the academic market (Nerad 1999). For these reasons, and because the ratio of Ph.D.s to available academic positions is increasing (Schillebeeckx et al. 2013), postdoctoral positions have nearly become a prerequisite for modern careers in ecology. The postdoctoral phase is clearly an important, and potentially exciting, time to develop the skills needed to succeed in an academic career. Yet the uncertainty of advancing successfully to the next career stage Ecology Postdocs in Academia: Primary Concerns and Possible Solutions

Microorganisms inhabit almost every environment, comprise the majority of diversity on Earth, are important in biogeochemical cycling, and may be vital to ecosystem responses to large-scale climatic change. In recent years, ecologists have begun to use rapidly advancing molecular techniques to address questions about microbial diversity, biogeography, and responses to environmental change. Studies of microbes in the environment generally focus on three broad objectives: determining which organisms are present, what their functional capabilities are, and which are active at any given time. However, comprehending the range of methodologies currently in use can be daunting. To provide an overview of environmental microbial sequence data collection and analysis approaches, we include case studies of microbiomes ranging from the human mouth to geothermal springs. We also suggest contexts in which each technique can be applied and highlight insights that result from their use.

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.

The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified basal area (BA) and densities of woody species and understory cover at nine sites in the Puna district on the Island of Hawai‘i, representing age gradients of native stand development on both ‘a’ā and pāhoehoe lava flows. On both flow types, BA of native species increased (from 5 to 50 m2/ha) and stem densities decreased (from 3700 to 2600 stems/ha) with increasing stand/flow age. Both native and introduced species compositions diverged between substrate types on older flows. We found that lowland wet native forests remain at least partially intact in several locations, but their functional and compositional integrity is increasingly compromised by invasion of nonnative species, such as Psidium cattleianum and Melastoma candidum, which become more common at sites greater than 300-yr old. This time period may represent a threshold, after which abiotic environmental conditions no longer constrain recruitment of introduced species. On older flows, nonnative stem densities swamped those of native species by an order of magnitude, with nonnative stems (height > 1.3 m) achieving densities as high as 18,000 stems/ha. In addition, all stands lacked recruitment of native woody species in the understory, suggesting that without management, the native componentsof these forests may soon no longer be self-sustaining. Patrones de Sucesion Primaria de Especies Nativas e Introducidas en los Bosques Muy Humedos del Este de Hawaii La mayoria de los bosques muy humedos de Hawaii han desaparecido; los fragmentos restantes se encuentran en las zonas orientales y de barlovento de las islas principales. Con el objetivo de mejorar nuestro conocimiento sobre los patrones sucesionales y de invasion en estos ecosistemas nativos, medimos el area basal (AB), la densidad de especies lenosas, y la cobertura del sotobosque en nueve areas de studio. Estas areas localizadas sobre formaciones volcanicas de tipo ‘a’ā y pāhoehoe en el distrito de Puna en la Isla de Hawai’i representan una cronosecuencia de desarrollo de rodal nativo. Sobre los dos tipos de formacion volcanica, el AB de las especies nativas aumento (de 5 a 50 m2/ha) y la densidad de troncos disminuyo (de 3.700 a 2.600 troncos/ha) con un aumento en la edad del rodal y de la formacion volcanica. Sobre los substratos mas antiguos, reportamos una divergencia en la composicion tanto de especies nativas como de las introducidas entre los dos tipos de lava volcanica. En algunos lugares, los bosques muy humedos permanecen en estado parcialmente intacto, pero su integridad funcional y composicional se encuentra cada vez mas comprometida por la invasion de especies no- nativas, como Psidium cattleianum y Melastoma candidum, que llegan a ser mas comunes en las areas mayores a los 300 anos. Este periodo posiblemente represente un umbral temporal, tras el cual el reclutamiento de especies introducidas deja de estar limitado por condiciones ambientales abioticas. Sobre las formaciones mas antiguas, la densidad de troncos no-nativos sobrepaso la de especies nativas por una orden de magnitud, con troncos no-nativos (de altura > 1.3 m) alcanzando densidades de 18,000 troncos/ha. Todos los rodales estudiados carecian de reclutamiento de especies lenosas nativas en el sotobosque, sugeriendo que la composicion nativa de estos bosques no es sostenible sin practicas de manejo activo.

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.

International audience; We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevance given the urgent need for interdisciplinary, geographical, and cross-sector collaboration to cope with growing challenges to the environment as well as the scientific community itself. Amidst the emergence of new international institutions, organizations, and meetings, GCIPs provide a stable international infrastructure for rapid and long-term coordination that can be accessed by any individual. This accessibility can be especially important for researchers early in their careers. Recent examples of early-career GCIPs complement an array of existing options for early-career scientists to improve skill sets, increase academic and social impact, and broaden career opportunities. We v www.esajournals.org 1 April 2015 v Volume 6(4) v Article 68 provide a number of examples of existing early-career initiatives that incorporate elements from the GCIPs approach, and highlight an in-depth case study from the ecological sciences: the International Network of Next-Generation Ecologists (INNGE), initiated in 2010 with support from the International Association for Ecology and 20 member institutions from six continents.

This paper was commissioned by the members of the Ecosphere Editorial Board to commemorate the ESA Centennial celebration.

The field of ecology is poised to take advantage of emerging technologies that facilitate the gathering, analyzing, and sharing of data, methods, and results. The concept of transparency at all stages of the research process, coupled with free and open access to data, code, and papers, constitutes "open science." Despite the many benefits of an open approach to science, a number of barriers to entry exist that may prevent researchers from embracing openness in their own work. Here we describe several key shifts in mindset that underpin the transition to more open science. These shifts in mindset include thinking about data stewardship rather than data ownership, embracing transparency throughout the data life-cycle and project duration, and accepting critique in public. Though foreign and perhaps frightening at first, these changes in thinking stand to benefit the field of ecology by fostering collegiality and broadening access to data and findings. We present an overview of tools and best practices that can enable these shifts in mindset at each stage of the research process, including tools to support data management planning and reproducible analyses, strategies for soliciting constructive feedback throughout the research process, and methods of broadening access to final research products.

Proficiency in mathematics and statistics is essential to modern ecological science, yet\ud few studies have assessed the level of quantitative training received by ecologists. To\ud do so, we conducted an online survey. The 937 respondents were mostly early-career\ud scientists who studied biology as undergraduates. We found a clear self-perceived\ud lack of quantitative training: 75% were not satisfied with their understanding of\ud mathematical models; 75% felt that the level of mathematics was “too low” in their\ud ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more\ud statistics classes. Respondents thought that 30% of classes in ecology-related degrees\ud should be focused on quantitative disciplines, which is likely higher than for most\ud existing programs. The main suggestion to improve quantitative training was to\ud relate theoretical and statistical modeling to applied ecological problems. Improving\ud quantitative training will require dedicated, quantitative classes for ecology-related\ud degrees that contain good mathematical and statistical practice.\ud

We surveyed endophytic fungal communities in leaves of a single tree species ( Metrosideros polymorpha ) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha , and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities.

Fungal leaf endophytes—nonpathogenic microfungi that live within plant leaves—are ubiquitous in land plants. Leaf endophytes and host plant genotypes may interact to determine plant disease severity. In a greenhouse inoculation experiment, we found that leaf endophyte species and Populus angustifolia genotypes both affected disease outcomes in plants inoculated with the necrotrophic leaf pathogen Drepanopeziza populi. Contrary to many studies showing endophytes conferring defense, all plant genotypes inoculated with the endophyte Penicillium sp. prior to inoculation with the pathogen D. populi were characterized by greater pathogen symptom severity than plants inoculated with the pathogen only. We quantified defense gene expression via qRT–PCR, but found no evidence that increased pathogen damage was related to differential expression of the assayed genes. A second endophyte, Truncatella angustata, which was previously found to reduce symptom severity of the biotrophic pathogen Melampsora in Populus trichocarpa, did not affect symptom severity of the necrotrophic pathogen D. populi or defense gene expression. Overall, our study highlights the variable effects of endophytes on pathogen symptom severity, and illustrates that plant genotypic variation can remain important for disease outcomes even in the presence of endophytes altering disease. Additional work is needed to elucidate the mechanism by which fungal leaf endophytes alter disease in their host plants.