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  • Other Sources  (48)
  • Nature Publishing Group  (48)
  • 2015-2019  (48)
  • 1
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    Quorum sensing signal–response systems in Gram-negative bacteria (2016)
    Nature Publishing Group
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    Publication Date: 2024-04-12
    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.
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  • 2
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    Advancing microbial sciences by individual-based modelling (2016)
    Nature Publishing Group
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    Publication Date: 2023-12-21
    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).
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  • 3
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    A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity (2015)
    Nature Publishing Group
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    Publication Date: 2023-11-29
    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.
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  • 4
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    Massive nitrous oxide emissions from the tropical South Pacific Ocean (2015)
    Nature Publishing Group
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    Publication Date: 2023-09-19
    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.
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  • 5
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    Multidrug efflux pumps: structure, function and regulation (2018)
    Nature Publishing Group
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    Publication Date: 2022-12-22
    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.
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  • 6
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    Complementary effects of species and genetic diversity on productivity and stability of sown grasslands (2015)
    Nature Publishing Group
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    Publication Date: 2022-09-21
    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.
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  • 7
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    Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf (2015)
    Nature Publishing Group
    In:  The ISME Journal, 9 (12). pp. 2551-2560.
    Details
    Publication Date: 2021-04-23
    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.
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  • 8
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    Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (11). pp. 856-860.
    Details
    Publication Date: 2021-04-23
    Description: Oceanic dissolved organic carbon (DOC) is an important carbon pool, similar in magnitude to atmospheric CO2, but the fate of its oldest forms is not well understood. Hot hydrothermal circulation may facilitate the degradation of otherwise un-reactive dissolved organic matter, playing an important role in the long-term global carbon cycle. The oldest, most recalcitrant forms of DOC, which make up most of oceanic DOC, can be recovered by solid-phase extraction. Here we present measurements of solid-phase extractable DOC from samples collected between 2009 and 2013 at seven vent sites in the Atlantic, Pacific and Southern oceans, along with magnesium concentrations, a conservative tracer of water circulation through hydrothermal systems. We find that magnesium and solid-phase extractable DOC concentrations are correlated, suggesting that solid-phase extractable DOC is almost entirely lost from solution through mineralization or deposition during circulation through hydrothermal vents with fluid temperatures of 212-401°C. In laboratory experiments, where we heated samples to 380°C for four days, we found a similar removal efficiency. We conclude that thermal degradation alone can account for the loss of solid-phase extractable DOC in natural hydrothermal systems, and that its maximum lifetime is constrained by the timescale of hydrothermal cycling, at about 40 million years
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  • 9
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    Water column methanotrophy controlled by a rapid oceanographic switch (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (5). pp. 378-382.
    Details
    Publication Date: 2020-11-23
    Description: Large amounts of the greenhouse gas methane are released from the seabed to the water column1, where it may be consumed by aerobic methanotrophic bacteria2. The size and activity of methanotrophic communities, which determine the amount of methane consumed in the water column, are thought to be mainly controlled by nutrient and redox dynamics3–7. Here, we report repeated measurements of methanotrophic activity and community size at methane seeps west of Svalbard, and relate them to physical water mass properties and modelled ocean currents. We show that cold bottom water, which contained a large number of aerobic methanotrophs, was displaced by warmer water with a considerably smaller methanotrophic community within days. Ocean current simulations using a global ocean/sea-ice model suggest that this water mass exchange is consistent with short-term variations in the meandering West Spitsbergen Current. We conclude that the shift from an offshore to a nearshore position of the current can rapidly and severely reduce methanotrophic activity in the water column. Strong fluctuating currents are common at many methane seep systems globally, and we suggest that they affect methane oxidation in the water column at other sites, too.
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  • 10
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    Diversity of key players in the microbial ecosystems of the human body (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 . p. 15920.
    Details
    Publication Date: 2020-11-09
    Description: Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.
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