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Describes the lives and interaction of animals and plants that inhabit the many worlds of water.

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon ( rrn ) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability. Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.

Climate and physiology shape biogeography, yet the range limits of species can rarely be ascribed to the quantitative traits of organisms 1 – 3 . Here we evaluate whether the geographical range boundaries of species coincide with ecophysiological limits to acquisition of aerobic energy 4 for a global cross-section of the biodiversity of marine animals. We observe a tight correlation between the metabolic rate and the efficacy of oxygen supply, and between the temperature sensitivities of these traits, which suggests that marine animals are under strong selection for the tolerance of low O 2 (hypoxia) 5 . The breadth of the resulting physiological tolerances of marine animals predicts a variety of geographical niches—from the tropics to high latitudes and from shallow to deep water—which better align with species distributions than do models based on either temperature or oxygen alone. For all studied species, thermal and hypoxic limits are substantially reduced by the energetic demands of ecological activity, a trait that varies similarly among marine and terrestrial taxa. Active temperature-dependent hypoxia thus links the biogeography of diverse marine species to fundamental energetic requirements that are shared across the animal kingdom. A tight coupling between metabolic rate, efficacy of oxygen supply and the temperature sensitivities of marine animals predicts a variety of geographical niches that better aligns with the distributions of species than models of either temperature or oxygen alone.

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions. Plankton communities in the top 150 m of the nutrient-depleted, oligotrophic global ocean that are most associated with carbon export include unexpected taxa, such as Radiolaria, alveolate parasites, and Synechococcus and their phages, and point towards potential functional markers predicting a significant fraction of the variability in carbon export in these regions. Oceanic plankton associated with carbon flux Using environmental and metagenomic data collected during the Tara Oceans expedition, this study examines the plankton communities that are most strongly associated with carbon export in the top 150 metres of the nutrient-depleted, oligotrophic global ocean. This work highlights some unexpected taxa as lineages strongly associated with carbon export, including Dinophyceae and Rhizaria, and alveolate parasites, in addition to Synechococcus and their phages, and suggests that the relative abundance of just a few bacterial and viral genes can predict most of the variability in carbon export in these regions.

There has been active debate over microbial life in Antarctic subglacial lakes owing to a paucity of direct observations from beneath the ice sheet and concerns about contamination in the samples that do exist; here the authors present the first geomicrobiological description of pristine water and surficial sediments from Subglacial Lake Whillans, and show that the lake water contains a diverse microbial community, many members of which are closely related to chemolithoautotrophic bacteria and archaea. Abundant microbes in subglacial Lake Whillans Whether there is microbial life in subglacial lakes in the Antarctic has been a matter of controversy, as early results were compromised when it was discovered that contamination may have occurred during drilling. Discovered less than a decade ago using satellite data, Lake Whillans lies beneath some 800 metres of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. In the first study to sample Antarctic subglacial waters directly, analysis of sediments obtained by the WISSARD drilling program shows that Lake Whillans' water contains more than 3,900 different types of bacteria and archaea, including one closely related to the nitrite oxidizing betaproteobacterium ' Candidatus Nitrotoga arctica', which comprised 13% of the sequence data. The lake waters contain a diverse range of metabolically active microorganisms, many of which seem to gain nutrients from the melting ice and from the rock and sediment beneath the ice. Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years 1 , but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale 2 , 3 , 4 . Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network 5 . The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes 2 , 4 that can mobilize elements from the lithosphere 6 and influence Southern Ocean geochemical and biological systems 7 .

Diatoms are one of the most ecologically successful classes of photosynthetic marine eukaryotes in the contemporary oceans. Over the past 30 million years, they have helped to moderate Earth's climate by absorbing carbon dioxide from the atmosphere, sequestering it via the biological carbon pump and ultimately burying organic carbon in the lithosphere. The proportion of planetary primary production by diatoms in the modern oceans is roughly equivalent to that of terrestrial rainforests. In photosynthesis, the efficient conversion of carbon dioxide into organic matter requires a tight control of the ATP/NADPH ratio which, in other photosynthetic organisms, relies principally on a range of plastid-localized ATP generating processes. Here we show that diatoms regulate ATP/NADPH through extensive energetic exchanges between plastids and mitochondria. This interaction comprises the re-routing of reducing power generated in the plastid towards mitochondria and the import of mitochondrial ATP into the plastid, and is mandatory for optimized carbon fixation and growth. We propose that the process may have contributed to the ecological success of diatoms in the ocean.

The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems 1 , 2 . However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications 3 , 4 . Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR–Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR–Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine. Analysis of 43,191 genomes obtained from publicly available marine bacterial and archaeal metagenome data provides insights into marine bacterial evolution, CRISPR–Cas defence and antibiotic resistance genes, and demonstrates the potential of marine metagenomes for biotechnological applications.