Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence

In mature soils, plant species and soil type determine the selection of root microbiota. Which of these two factors drives rhizosphere selection in barren substrates of developing desert soils has, however, not yet been established. Chronosequences of glacier forelands provide ideal natural environments to identify primary rhizosphere selection factors along the changing edaphic conditions of a developing soil. Here, we analyze changes in bacterial diversity in bulk soils and rhizospheres of a pioneer plant across a High Arctic glacier chronosequence. We show that the developmental stage of soil strongly modulates rhizosphere community assembly, even though plant-induced selection buffers the effect of changing edaphic factors. Bulk and rhizosphere soils host distinct bacterial communities that differentially vary along the chronosequence. Cation exchange capacity, exchangeable potassium, and metabolite concentration in the soil account for the rhizosphere bacterial diversity. Although the soil fraction (bulk soil and rhizosphere) explains up to 17.2% of the variation in bacterial microbiota, the soil developmental stage explains up to 47.7% of this variation. In addition, the operational taxonomic unit (OTU) co-occurrence network of the rhizosphere, whose complexity increases along the chronosequence, is loosely structured in barren compared with mature soils, corroborating our hypothesis that soil development tunes the rhizosphere effect

The Internal Microenvironment of the Symbiotic Jellyfish Cassiopea sp. From the Red Sea

<jats:p>The characterization of the internal microenvironment of symbiotic marine invertebrates is essential for a better understanding of the symbiosis dynamics. Microalgal symbionts (of the family: Symbiodiniaceae) influence diel fluctuations of <jats:italic>in host</jats:italic> O<jats:sub>2</jats:sub> and pH conditions through their metabolic activities (i.e., photosynthesis and respiration). These variations may play an important role in driving oxygen budgets and energy demands of the holobiont and its responses to climate change. <jats:italic>In situ</jats:italic> measurements using microsensors were used to resolve the O<jats:sub>2</jats:sub> and pH diel fluctuations in the oral arms of non-calcifying cnidarian model species <jats:italic>Cassiopea</jats:italic> sp. (the “upside-down jellyfish”), which has an obligatory association with Symbiodiniaceae. Before sunrise, the internal O<jats:sub>2</jats:sub> and pH levels were substantially lower than those in ambient seawater conditions (minimum average levels: 61.92 ± 5.06 1SE μmol O<jats:sub>2</jats:sub> L<jats:sup>–1</jats:sup> and 7.93 ± 0.02 1SE pH units, respectively), indicating that conditions within <jats:italic>Cassiopea’s</jats:italic> oral arms were acidified and hypoxic relative to the surrounding seawater. Measurements performed during the afternoon revealed hyperoxia (maximum average levels: 546.22 ± 16.45 1SE μmol O<jats:sub>2</jats:sub> L<jats:sup>–1</jats:sup>) and internal pH similar to ambient levels (8.61 ± 0.02 1SE pH units). The calculated gross photosynthetic rates of <jats:italic>Cassiopea</jats:italic> sp. were 0.04 ± 0.013 1SE nmol cm<jats:sup>–2</jats:sup> s<jats:sup>–1</jats:sup> in individuals collected at night and 0.08 ± 0.02 1SE nmol cm<jats:sup>–2</jats:sup> s<jats:sup>–1</jats:sup> in individuals collected during the afternoon.</jats:p&gt

Toward unrestricted use of public genomic data.

Despite some notable progress in data sharing policies and practices, restrictions are still often placed on the open and unconditional use of various genomic data after they have received official approval for release to the public domain or to public databases. These restrictions, which often conflict with the terms and conditions of the funding bodies who supported the release of those data for the benefit of the scientific community and society, are perpetuated by the lack of clear guiding rules for data usage. Existing guidelines for data released to the public domain recognize but fail to resolve tensions between the importance of free and unconditional use of these data and the “right” of the data producers to the first publication. This self-contradiction has resulted in a loophole that allows different interpretations and a continuous debate between data producers and data users on the use of public data. We argue that the publicly available data should be treated as open data, a shared resource with unrestricted use for analysis, interpretation, and publication