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Lineage dynamics of the endosymbiotic cell type in the soft coralXenia 期刊论文
NATURE, 2020
作者:  Lewnard, Joseph A.;  Lo, Nathan C.;  Arinaminpathy, Nimalan;  Frost, Isabel;  Laxminarayan, Ramanan
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

Many corals harbour symbiotic dinoflagellate algae. The algae live inside coral cells in a specialized membrane compartment known as the symbiosome, which shares the photosynthetically fixed carbon with coral host cells while host cells provide inorganic carbon to the algae for photosynthesis(1). This endosymbiosis-which is critical for the maintenance of coral reef ecosystems-is increasingly threatened by environmental stressors that lead to coral bleaching (that is, the disruption of endosymbiosis), which in turn leads to coral death and the degradation of marine ecosystems(2). The molecular pathways that orchestrate the recognition, uptake and maintenance of algae in coral cells remain poorly understood. Here we report the chromosome-level genome assembly of aXeniaspecies of fast-growing soft coral(3), and use this species as a model to investigate coral-alga endosymbiosis. Single-cell RNA sequencing identified 16 cell clusters, including gastrodermal cells and cnidocytes, inXeniasp. We identified the endosymbiotic cell type, which expresses a distinct set of genes that are implicated in the recognition, phagocytosis and/or endocytosis, and maintenance of algae, as well as in the immune modulation of host coral cells. By couplingXeniasp. regeneration and single-cell RNA sequencing, we observed a dynamic lineage progression of the endosymbiotic cells. The conserved genes associated with endosymbiosis that are reported here may help to reveal common principles by which different corals take up or lose their endosymbionts.


  
Introduced herbivores restore Late Pleistocene ecological functions 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (14) : 7871-7878
作者:  Lundgren, Erick J.;  Ramp, Daniel;  Rowan, John;  Middleton, Owen;  Schowanek, Simon D.;  Sanisidro, Oscar;  Carroll, Scott P.;  Davis, Matt;  Sandom, Christopher J.;  Svenning, Jens-Christian;  Wallach, Arian D.
收藏  |  浏览/下载:10/0  |  提交时间:2020/05/13
megafauna  novel ecosystems  functional ecology  restoration ecology  invasion  
Rebuilding marine life 期刊论文
NATURE, 2020, 580 (7801) : 39-51
作者:  Carlos M. Duarte;  Susana Agusti;  Edward Barbier;  Gregory L. Britten;  Juan Carlos Castilla;  Jean-Pierre Gattuso;  Robinson W. Fulweiler;  Terry P. Hughes;  Nancy Knowlton;  Catherine E. Lovelock;  Heike K. Lotze;  Milica Predragovic;  Elvira Poloczanska;  Callum Roberts;  Boris Worm
收藏  |  浏览/下载:12/0  |  提交时间:2020/05/13

Sustainable Development Goal 14 of the United Nations aims to "conserve and sustainably use the oceans, seas and marine resources for sustainable development". Achieving this goal will require rebuilding the marine life-support systems that deliver the many benefits that society receives from a healthy ocean. Here we document the recovery of marine populations, habitats and ecosystems following past conservation interventions. Recovery rates across studies suggest that substantial recovery of the abundance, structure and function of marine life could be achieved by 2050, if major pressures-including climate change-are mitigated. Rebuilding marine life represents a doable Grand Challenge for humanity, an ethical obligation and a smart economic objective to achieve a sustainable future.


  
Tracking of marine predators to protect Southern Ocean ecosystems 期刊论文
NATURE, 2020
作者:  Kim, Eugene;  Kerssemakers, Jacob;  Shaltiel, Indra A.;  Haering, Christian H.;  Dekker, Cees
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/03

Tracking data from 17 marine predator species in the Southern Ocean are used to identify Areas of Ecological Significance, the protection of which could help to mitigate increasing pressures on Southern Ocean ecosystems.


Southern Ocean ecosystems are under pressure from resource exploitation and climate change(1,2). Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40 degrees S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.


  
Clades of huge phages from across Earth's ecosystems 期刊论文
NATURE, 2020, 578 (7795) : 425-+
作者:  Zhang, Bing;  Ma, Sai;  Rachmin, Inbal;  He, Megan;  Baral, Pankaj;  Choi, Sekyu;  Goncalves, William A.;  Shwartz, Yulia;  Fast, Eva M.;  Su, Yiqun;  Zon, Leonard I.;  Regev, Aviv;  Buenrostro, Jason D.;  Cunha, Thiago M.;  Chiu, Isaac M.
收藏  |  浏览/下载:37/0  |  提交时间:2020/07/03

Bacteriophages typically have small genomes(1) and depend on their bacterial hosts for replication(2). Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth'  s ecosystems.


Genomic analyses of major clades of huge phages sampled from across Earth'  s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR-Cas systems and translation-relevant genes.


  
Land-use history impacts functional diversity across multiple trophic groups 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (3) : 1573-1579
作者:  Le Provost, Gaetane;  Badenhausser, Isabelle;  Le Bagousse-Pinguet, Yoann;  Clough, Yann;  Henckel, Laura;  Violle, Cyrille;  Bretagnolle, Vincent;  Roncoroni, Marilyn;  Manning, Peter;  Gross, Nicolas
收藏  |  浏览/下载:15/0  |  提交时间:2020/05/13
agricultural ecosystems  biodiversity loss  functional diversity  grasslands  land-use changes  
Ocean acidification does not impair the behaviour of coral reef fishes 期刊论文
NATURE, 2020, 577 (7790) : 370-+
作者:  Clark, Timothy D.;  Raby, Graham D.;  Roche, Dominique G.;  Binning, Sandra A.;  Speers-Roesch, Ben;  Jutfelt, Fredrik;  Sundin, Josefin
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

The partial pressure of CO2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems(1-3). Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers(4,5) that have reported profound behavioural and sensory impairments-for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that-in contrast to previous studies-end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left-right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans.


  
Giant virus diversity and host interactions through global metagenomics 期刊论文
NATURE, 2020: 1-+
作者:  Su, Jie;  Morgani, Sophie M.;  David, Charles J.;  Wang, Qiong;  Er, Ekrem Emrah;  Huang, Yun-Han;  Basnet, Harihar;  Zou, Yilong;  Shu, Weiping;  Soni, Rajesh K.;  Hendrickson, Ronald C.;  Hadjantonakis, Anna-Katerina;  Massague, Joan
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Analysis of metagenomics data revealed that large and giant viruses are globally widely distributed and are associated with most major eukaryotic lineages.


Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth'  s biomes.


  
Importance and vulnerability of the world's water towers 期刊论文
NATURE, 2020, 577 (7790) : 364-+
作者:  Krebs, John R.;  Hassell, Michael
收藏  |  浏览/下载:49/0  |  提交时间:2020/04/16

Mountains are the water towers of the world, supplying a substantial part of both natural and anthropogenic water demands(1,2). They are highly sensitive and prone to climate change(3,4), yet their importance and vulnerability have not been quantified at the global scale. Here we present a global water tower index (WTI), which ranks all water towers in terms of their water-supplying role and the downstream dependence of ecosystems and society. For each water tower, we assess its vulnerability related to water stress, governance, hydropolitical tension and future climatic and socioeconomic changes. We conclude that the most important (highest WTI) water towers are also among the most vulnerable, and that climatic and socio-economic changes will affect them profoundly. This could negatively impact 1.9 billion people living in (0.3 billion) or directly downstream of (1.6 billion) mountainous areas. Immediate action is required to safeguard the future of the world'  s most important and vulnerable water towers.


  
Temperature change as a driver of spatial patterns and long-term trends in chironomid (Insecta: Diptera) diversity 期刊论文
GLOBAL CHANGE BIOLOGY, 2019
作者:  Engels, Stefan;  Medeiros, Andrew S.;  Axford, Yarrow;  Brooks, Stephen J.;  Heiri, Oliver;  Luoto, Tomi P.;  Nazarova, Larisa;  Porinchu, David F.;  Quinlan, Roberto;  Self, Angela E.
收藏  |  浏览/下载:14/0  |  提交时间:2019/11/27
Arctic  biodiversity  climate warming  freshwater ecosystems  insects  palaeoecology  Quaternary