ALBERT

Description: Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy.

Description: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage–CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).

Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.

Description: Nitrous oxide is a potent greenhouse gas and a key compound in stratospheric ozone depletion. In the ocean, nitrous oxide is produced at intermediate depths through nitrification and denitrification, in particular at low oxygen concentrations. Although a third of natural emissions of nitrous oxide to the atmosphere originate from the ocean, considerable uncertainties in the distribution and magnitude of the emissions still exist. Here we present high-resolution surface measurements and vertical profiles of nitrous oxide that include the highest reported nitrous oxide concentrations in marine surface waters, suggesting that there is a hotspot of nitrous oxide emissions in high-productivity upwelling ecosystems along the Peruvian coast. We estimate that off Peru, the extremely high nitrous oxide supersaturations we observed drive a massive efflux of 0.2–0.9 Tg of nitrogen emitted as nitrous oxide per year, equivalent to 5–22% of previous estimates of global marine nitrous oxide emissions. Nutrient and gene abundance data suggest that coupled nitrification–denitrification in the upper oxygen minimum zone and transport of resulting nitrous oxide to the surface by upwelling lead to the high nitrous oxide concentrations. Our estimate of nitrous oxide emissions from the Peruvian coast surpasses values from similar, highly productive areas.

Description: Palaeoclimate records and numerical model simulations indicate that changes in tropical and subtropical sea surface temperatures and in the annual average position of the intertropical convergence zone are linked to high-latitude climate changes on millennial to glacial–interglacial timescales. It has recently been suggested that cooling in the high latitudes associated with abrupt climate-change events is evident primarily during the northern hemisphere winter, implying increased seasonality at these times8. However, it is unclear whether such a seasonal bias also exists for the low latitudes. Here we analyse the Mg/Ca ratios of surface-dwelling foraminifera to reconstruct sea surface temperatures in the northeastern Gulf of Mexico for the past 300,000 years. We suggest that sea surface temperatures are controlled by the migration of the northern boundary of the Atlantic Warm Pool, and hence the position of the intertropical convergence zone during boreal summer, and are relatively insensitive to winter conditions. Our results suggest that summer Atlantic Warm Pool expansion is primarily affected by glacial–interglacial variability and low-latitude summer insolation. Because a clear signature of rapid climate-change events, such as the Younger Dryas cold event, is lacking in our record, we conclude that high-latitude events seem to influence only the winter Caribbean climate conditions, consistent with the hypothesis of extreme northern-hemisphere seasonality during abrupt cooling events.

Description: Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.

Description: Plant species diversity regulates the productivity1–3 and stability2,4 of natural ecosystems, along with their resilience to disturbance5,6. The influence of species diversity on the productivity of agronomic systems is less clear7–10. Plant genetic diversity is also suspected to influence ecosystem function3,11–14, although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.

Description: Sexual mimicry among animals is widespread, but does it impart a fertilization advantage in the widely accepted ‘sneak–guard’ model of sperm competition? Here we describe field results in which a dramatic facultative switch in sexual phenotype by sneaker-male cuttlefish leads to immediate fertilization success, even in the presence of the consort male. These results are surprising, given the high rate at which females reject copulation attempts by males, the strong mate-guarding behaviour of consort males, and the high level of sperm competition in this complex mating system

Description: The symbiotic association of corals and unicellular algae of the genus Symbiodinium in the southern Persian/Arabian Gulf (PAG) display an exceptional heat tolerance, enduring summer peak temperatures of up to 36 °C. As yet, it is not clear whether this resilience is related to the presence of specific symbiont types that are exclusively found in this region. Therefore, we used molecular markers to identify the symbiotic algae of three Porites species along 〉1000 km of coastline in the PAG and the Gulf of Oman and found that a recently described species, Symbiodinium thermophilum, is integral to coral survival in the southern PAG, the world’s hottest sea. Despite the geographic isolation of the PAG, we discovered that representatives of the S. thermophilum group can also be found in the adjacent Gulf of Oman providing a potential source of thermotolerant symbionts that might facilitate the adaptation of Indian Ocean populations to the higher water temperatures expected for the future. However, corals from the PAG associated with S. thermophilum show strong local adaptation not only to high temperatures but also to the exceptionally high salinity of their habitat. We show that their superior heat tolerance can be lost when these corals are exposed to reduced salinity levels common for oceanic environments elsewhere. Consequently, the salinity prevailing in most reefs outside the PAG might represent a distribution barrier for extreme temperature-tolerant coral/Symbiodinium associations from the PAG.