Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

Abstract

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for “Reporting” and “Serving” data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7^th Framework Programme “Ocean of Tomorrow”, and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

Background

An immense wealth of genetic, functional and morphological diversity in marine ecosystems remains unexplored, offering the potential for substantial scientific and biotechnological discoveries. Indeed, significant interest in this area has led to large-scale initiatives, such as Tara Oceans [1], the Global Ocean Survey [2] and Malaspina [3], that target the exploration of marine biodiversity on planetary scales. While the shared goal of such initiatives is the development of an understanding of the composition and ecology of marine microbial ecosystems, each focuses on different parts of the taxonomic breadth of ocean life and only a subset of ocean ecosystems, such as epi- meso- and bathypelagic systems. Ongoing and future marine survey projects will add value to these explorations and will continue to build a powerful marine data infrastructure from which ecosystems biology and biotechnology will derive benefit. Prerequisite for the successful exploitation of acquired data are standards that enable interoperability in the data infrastructure.

Just as marine studies span many disciplines (e.g. biological, oceanographic, molecular), use of data from marine studies requires approaches that traverse the many disciplines, asking questions, for example, of species distribution, physical oceanographic parameters, molecular biology and data licensing. Each discipline has established infrastructure and best practice for the dissemination of its data, including open data repositories, reporting and data standards and discovery and analysis portals. However, there remain major barriers when data are to be used across disciplines that relate to a lack of interoperability between standards and the lack of a consistent environment for the discovery and retrieval of data.

The Marine Microbial Biodiversity, Bioinformatics, Biotechnology Project (Micro B3) [4] unites intensive oceanographic monitoring, thorough biodiversity studies and high-throughput DNA sequencing of marine genomes, metagenomes and pan-genomes. The project addresses interdisciplinary needs in marine ecosystems biology and biotechnology by considering established best practice within the disciplines and deriving practical least-change means to align practices. Recognising that it is non-trivial to influence deeply-rooted working practices established over decades, we have delivered an extensive programme of workshop-based discussions amongst representatives of the disciplines [22,23].

This effort led to the development of two standards described here. First, the M2B3 Reporting Standard defines and describes fields of information to be made available with marine data sets. Second, the M2B3 Service Standard defines and describes a software interface through which hosts of marine data, such as the public data repositories, can present their marine data holdings.

The resulting standards were used by marine sampling stations and cruises participating in the Micro B3 sampling campaign, Ocean Sampling Day (OSD) [5], a simultaneous world-scale sample and contextual data collection to investigate dynamics and functions of marine microbial diversity. We believe that our work will also be of value to other marine surveys in the future.

M2B3 Reporting Standard

We have developed the M2B3 Reporting Standard to support data collection and dissemination for those involved in marine microbial sampling. The standard, shown in full in Tables 1,2,3,4,5,6,7 spans the biodiversity, molecular and oceanographic domains and adopts existing standards of each discipline with their mandatory, recommended and optional descriptors (fields of information) (see Figure 1). It represents a unique intersection of existing reporting requirements across all three domains.

Table 1 M2B3 Reporting Standard about an investigation effort

Table 2 M2B3 Reporting Standard about a sampling event

Table 3 M2B3 Reporting Standard about a sample

Table 4 M2B3 Reporting Standard about the sample environmental context

Table 5 M2B3 Reporting Standard about environmental measurements

Table 6 M2B3 Reporting Standard about organisms in a sample

Table 7 M2B3 Reporting Standard about environmental measurement processes

Figure 1

M2B3 Reporting Standard descriptors schematically depicted on the junction of three disciplines, adopting existing standards of each domain.

We have been strongly guided in this work by the existing standards MEDIN [6], MIxS [7] and Darwin Core [8], the expertise of the Tara Oceans project teams and the International Census of Marine Microbes (ICoMM) project [9], and knowledge of community-established reporting practice into public data archives bestowed by experts from the biodiversity, oceanographic and molecular domain.

The core of the M2B3 Reporting Standard is the M2B3 checklist, (see Figure 2). This core represents the minimal mandatory reporting requirement and consists of descriptors essential to oceanographic, biodiversity and molecular domains, representing research on microbial diversity and function in the marine environment. Marine scientists should be able to report this minimum contextual information about each marine microbial sample irrespective of their scientific expertise and resources available for the sampling.

Figure 2

Mandatory and recommended information of the M2B3 Reporting Standard; descriptors are split into six categories represented by coloured triangles, where mandatory descriptors are in the dark-shaded area and recommended information elements are in the light-shaded area. Environmental measurements in the ENVIRONMENT section are further specified in Figure 3.

The M2B3 Reporting Standard includes a set of recommended descriptors (see Figure 2), provision of which brings each marine microbial sample into a rich environmental context and allows better ecological interpretation and experimental reproducibility. The standard’s environmental parameters are recommended by the Micro B3 Consortium for description of the environmental landscape of each epipelagic microbial sample (see Figure 3). Here, we have taken an approach including descriptors that draw a balance between analysis requirements-driven methods and current reporting practice in marine microbial sampling. In the requirements-driven approach we analysed several use cases from the area of diatom biology and marine prokaryotic biodiversity. Collated environmental parameters, recorded and reported in these studies in order to answer the scientific questions posed in the studies, represent the optimal list of environmental variables to be measured at the time of microbial sample collection from the epipelagic zone. The current sampling practice-driven approach is the pragmatic counterpart, where environmental variables were identified based on current marine sampling practice surveys and consultations with experts from European marine stations with established long-term sea monitoring programs and a wealth of expertise, such as Western Channel Observatory in the UK, Station Biologique de Roscoff in France, the Stazione Zoologica in Naples, Italy, or the Biological Institute Helgoland (BAH) of the Alfred Wegener Institute, the Helmholtz Centre for Polar and Marine Research in Germany.

Figure 3

Mandatory (in the dark green area) and recommended (in the light green area) environmental measurements of the M2B3 Reporting Standard.

All mandatory and recommended information is described in detail in Tables 1,2,3,4,5,6,7 including specification relating to usage, formal requirements for structure, indication of appropriate units, where applicable, and an example. Descriptors are split for easy navigation into six categories: (1) the marine investigation effort, (2) the sample-taking event, (3) sample-specific details, (4a) the environmental context of the sample, (4b) environmental measurements, (5) marine species found in the sample and (6) description of environmental measurement processes. Descriptors of each conceptual category are prefixed with the category name. Table 4 specifies a broad and local environmental context of a sample including required minimum of measured environmental parameters. Table 5 focuses on specific environmental parameters that complement the fields in Table 4. Table 7 defines how environmental measurements are captured. The logical relationship between the environmental measurement, measurement description and measurement values is summarised in Figure 4.

Figure 4

The logical connection between environmental measurements (Table 5 ), recording of the measurements (Table 7 ) and measured values, shown on the example of three environmental parameters – salinity, nitrate and carbon organic particulate (POC).

M2B3 Reporting standard compliance

It is worth noting that if all mandatory descriptors from the M2B3 Reporting Standard are reported by a sampling station or a cruise, then a data management centre is frequently able to infer additional descriptors available from the public record. In one example, relating to OSD, the Micro B3 Information System (Micro B3 IS) [10] and the OSD coordinators are able to infer additional descriptors available from public data archives, such as the Data Publisher for Earth and Environmental Science (PANGAEA) for environmental data [11,12] and the European Nucleotide Archive (ENA) for molecular data [13,14]. The additional information can be added post hoc for all samples acquired within the OSD campaign since the campaign has standardised and published sampling protocols and a Registry of OSD stations and cruises [15]. The inferred descriptors include, for instance, a sample catalogue number and collection code assigned by the bio-archiving institution where the OSD samples will be centrally deposited. In a second example that applies very broadly across marine samples, remotely sensed data (such as cloud cover, air temperature and wind conditions) can be connected to appropriate records based upon geospatial fields.

Combining information compliant with the M2B3 Reporting Standard from marine sampling laboratories with inferred information has two major advantages: (1) it significantly reduces the reporting burden for the marine sampling laboratories and (2) it ensures that OSD data records created at the molecular data archive will be compliant with the MIxS molecular data standard, Version 4 [16], OSD data records created at the oceanographic data archive will be compliant with the oceanographic Common Data Index (CDI), Version 3 [17] and OSD data records created at the biodiversity data archive will be compliant with the biodiversity OBIS Schema, Version 1.1 [18].

M2B3 service standard

Six descriptors from the M2B3 Reporting Standard are central to data interoperability across disciplines. These descriptors provide the basis for connecting data points from one discipline to data points in another and are thus the indices upon which data resources providing services must present their data. The interoperability descriptors are: INVESTIGATION_Site, INVESTIGATION_Platform, EVENT_Date/Time, EVENT_Longitude, EVENT_Latitude and SAMPLE_Depth.

In order for users of marine data to discover and access data, there is a need for these fields of information to be made searchable in a single and consistent way across relevant data resources.

We define the M2B3 Service Standard as a standardised set of informatics methods through which marine data can be discovered in data resources. The six interoperability descriptors are presented by a compliant data resource using a programmatic service interface that follows Open Geospatial Consortium (OGC) standards, the Web Map Service (WMS), Web Feature Service (WFS) and/or the OpenSearch protocol. To date, the European Nucleotide Archive, European Ocean Biogeographic Information System (EurOBIS) [19,20], Micro B3 Information System, PANGAEA and SeaDataNet [21] have committed to supporting the M2B3 Service Standard for OSD data.

Conclusions

The M2B3 Reporting Standard combines reporting requirements of three disciplines. Compliance with the standard ensures that the collected data can be correctly directed to and stored in their respective domain-specific data archives, which are the ENA for molecular data and PANGAEA for environmental data and morphology-based biodiversity data. Compliance with the standard allows PANGAEA to create a condensed metadata summary and share it with pan-European oceanographic and biodiversity information networks, managed by SeaDataNet and EurOBIS, respectively. Micro B3 IS and other data resources compliant with the M2B3 Service standard can discover marine data compliant with the M2B3 Reporting Standard.

During its preparation, development of the M2B3 Reporting Standard and the M2B3 Service Standard allowed experts from the oceanographic, biodiversity and molecular disciplines to review current working practice, to extract and formulate what is essential and universal and to find common ground. Adoption of the M2B3 Reporting Standard will require a similar effort from the marine science community, as already started with the OSD sampling marine laboratories. The ultimate reward will be a unique collection of standardised marine data for the exploration of ecosystem biology and the advance of biotechnology.