A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community

AtlantOS Deliverable 3.8: OceanSITES Networking Report

During the course of AtlantOS, our ability to provide biogeochemical (BGC) time series and Eulerian data which is of sufficient quality and quantity to approach basin-scale capacity has improved in a major way in some areas but has declined or not progressed in others. Indeed, the increased coordination achieved through AtlantOS has both increased our capacity to collectively further a basin-scale operation, and revealed new challenges in implementation. These outcomes are synthesised in this report to improve future planning for Eulerian capacities in BGC observation. Areas of significant progress 1. Development of capacity for emerging BGC variables 2. Establishment of a system for developing “Best practice” recording. 3. Transatlantic MOU with Canada 4. Data management and dissemination The ways to address the areas in which progress has not been made are conceptually simple but practically demanding. In all cases this needs to be carried out at the global scale and therefore under the auspices of OceanSITES. A coherent system which can provide data of sufficient quality and quantity to address societal needs cannot be achieved in isolation by any one Nation state or by Europe and must not be restricted by discipline. It will become self-evident that such an integrated approach will lead to a system which performs at a much higher level than the sum of its component parts. With continuous pressure from the European Commission, further and additional support from member states, continuing political and scientific dialogue with South Atlantic countries and strong management encouragement at all levels, the establishment of an effective eulerian observatory network is anticipated within the coming decade

Towards a Best Practice for Developing Best Practices in Ocean Observation (BP4BP): Supporting Methodological Evolution through Actionable Documentation

IOC Manuals and Guides, 84 Abstract Ever-increasing complexity and multi-dimensionality of ocean investigations present a challenge for the ocean community as we collaboratively (co-)develop methods to research, monitor, and use our oceans. To support transparent sharing of methods, and ultimately agree on best practices in ocean research, operations, and application, the IOC Ocean Best Practices System (OBPS) was initially developed as an Ocean Data Standards project deliverable of the International Oceanographic Data Exchange (IODE) who in 2017 joined with the AtlantOS/ODIP/RCN Best Practices Working Group (BPWG) to develop it into a System. In 2019 the IOC Ocean Best Practices System was approved as a UNESCO/Intergovernmental Oceanographic Commission (IOC) Project, jointly funded by the IODE and GOOS Programmes. In this document, we provide guidance on how to best use the OBPS templates, allowing greater discovery, machine readability, sharing, and understandability of methods and best practices. We clarify how to optimally populate the different sections of an OBPS template, and describe how those sections support the evolution of each OBPS submission, towards a global best practice. Further, we discuss some general challenges in developing methods into community-accepted best practices. While this document focuses on the OBPS, it also offers a perspective on the general challenge of structuring and harmonising method documentation. We invite the community to provide feedback on this document (link to Community review), to contribute towards a generalised best practice for advanced methodological management across the ocean community

Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes

Background: DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated. Results: We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool. Conclusions: Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data

Drivers of pelagic and benthic microbial communities on Central Arctic seamounts

Seamounts are abundant features on the seafloor that serve as hotspots and barriers for the dispersal of benthic organisms. The primary focus of seamount ecology has typically been on the composition and distribution of faunal communities, with far less attention given to microbial communities. Here, we investigated the microbial communities in the water column (0-3400 m depth) and sediments (619-3883 m depth, 0-16 cm below seafloor) along the ice-covered Arctic ridge system called the Langseth Ridge. We contextualized the microbial community composition with data on the benthic trophic state (i.e., organic matter, chlorophyll-a content, and porewater geochemistry) and substrate type (i.e., sponge mats, sediments, basaltic pebbles). Our results showed slow current velocities throughout the water column, a shift in the pelagic microbial community from a dominance of Bacteroidia in the 0-10 m depth towards Proteobacteria and Nitrososphaeria below the epipelagic zone. In general, the pelagic microbial communities showed a high degree of similarity between the Langseth Ridge seamounts to a northern reference site. The only notable differences were decreases in richness between ~600 m and the bottom waters (~10 m above the seafloor) that suggest a pelagic-benthic coupling mediated by filter feeding of sponges living on the seamount summits. On the seafloor, the sponge spicule mats, and polychaete worms were the principal source of variation in sedimentary biogeochemistry and the benthic microbial community structure. The porewater signature suggested that low organic matter degradation rates are accompanied by a microbial community typical of deep-sea oligotrophic environments, such as Proteobacteria, Acidimicrobiia, Dehalococcoidia, Nitrospira, and archaeal Nitrososphaeria. The combined analysis of biogeochemical parameters and the microbial community suggests that the sponges play a significant role for pelagic-benthic coupling and acted as ecosystem engineers on the seafloor of ice-covered seamounts in the oligotrophic central Arctic Ocean

Megx.net: integrated database resource for marine ecological genomics

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net

Recurrent patterns of microdiversity in a temperate coastal marine environment

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 12 (2018): 237–252, doi:10.1038/ismej.2017.165.Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.PLB is supported by the European Research Council Advanced Investigator grant ABYSS 294757 to Antje Boetius. AF-G is supported by the European Union’s Horizon 2020 research and innovation program (Blue Growth: Unlocking the potential of Seas and Oceans) under grant agreement no. (634486) (project acronym INMARE). This study was funded by the Max Planck Society. Further support by the Department of Energy Joint Genome Institute (CSP COGITO) and DFG (FOR2406) is acknowledged by HT (TE 813/2-1) and RA (Am 73/9-1)

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Background The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, ‘omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO’s growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings

AtlantOS Deliverable 6.2: Roadmap for emerging networks

Whilst the AtlantOS project is directed towards bringing together the existing, but currently disparate observing programmes in the Atlantic Ocean, there are still some gaps in terms of requirements for addressing the collection and curation of data around the Essential Ocean Variables. This deliverable will identify gaps and emerging observing networks. Here we use the term emerging network to classify science areas that are starting to gain importance with respect to EOV’s and their measurement and curation, or are existing small scale programmes or communities that might become more important in the future if we can find means of enhancing the collaboration among investigators/groups, increasing resources to the area or using new technological developments. In the AtlantOS project we have identified a number of areas in which there are gaps in our knowledge and where opportunities exist to enhance current small-scale networks. The scope of this document is to assess these networks, based on where we are now and where the networks could be in three and ten years’ time, respectively. An assessment of the state of the existing networks is useful to identify the level of international organisation and potential for further development in the future. We identify opportunities where synergies are possible with more established global projects, and where small levels of investment in resource and time for governance and coordination can productively and realistically develop the networks. We also identify if there are ways to develop coordinated approaches to metrology technology development. For this analysis, the networks have been allocated to one of the three groups outlined below