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Recycling and metabolic flexibility dictate life in the lower oceanic crust 期刊论文
NATURE, 2020, 579 (7798) : 250-+
作者:  Zhou, Peng;  Yang, Xing-Lou;  Wang, Xian-Guang;  Hu, Ben;  Zhang, Lei;  Zhang, Wei;  Si, Hao-Rui;  Zhu, Yan;  Li, Bei;  Huang, Chao-Lin;  Chen, Hui-Dong;  Chen, Jing;  Luo, Yun;  Guo, Hua;  Jiang, Ren-Di;  Liu, Mei-Qin;  Chen, Ying;  Shen, Xu-Rui;  Wang, Xi;  Zheng, Xiao-Shuang;  Zhao, Kai;  Chen, Quan-Jiao;  Deng, Fei;  Liu, Lin-Lin;  Yan, Bing;  Zhan, Fa-Xian;  Wang, Yan-Yi;  Xiao, Geng-Fu;  Shi, Zheng-Li
收藏  |  浏览/下载:37/0  |  提交时间:2020/05/13

The lithified lower oceanic crust is one of Earth'  s last biological frontiers as it is difficult to access. It is challenging for microbiota that live in marine subsurface sediments or igneous basement to obtain sufficient carbon resources and energy to support growth(1-3) or to meet basal power requirements(4) during periods of resource scarcity. Here we show how limited and unpredictable sources of carbon and energy dictate survival strategies used by low-biomass microbial communities that live 10-750 m below the seafloor at Atlantis Bank, Indian Ocean, where Earth'  s lower crust is exposed at the seafloor. Assays of enzyme activities, lipid biomarkers, marker genes and microscopy indicate heterogeneously distributed and viable biomass with ultralow cell densities (fewer than 2,000 cells per cm(3)). Expression of genes involved in unexpected heterotrophic processes includes those with a role in the degradation of polyaromatic hydrocarbons, use of polyhydroxyalkanoates as carbon-storage molecules and recycling of amino acids to produce compounds that can participate in redox reactions and energy production. Our study provides insights into how microorganisms in the plutonic crust are able to survive within fractures or porous substrates by coupling sources of energy to organic and inorganic carbon resources that are probably delivered through the circulation of subseafloor fluids or seawater.


  
Global-scale human impact on delta morphology has led to net land area gain 期刊论文
NATURE, 2020, 577 (7791) : 514-+
作者:  Nienhuis, J. H.;  Ashton, A. D.;  Edmonds, D. A.;  Hoitink, A. J. F.;  Kettner, A. J.;  Rowland, J. C.;  Tornqvist, T. E.
收藏  |  浏览/下载:8/0  |  提交时间:2020/05/13

River deltas rank among the most economically and ecologically valuable environments on Earth. Even in the absence of sea-level rise, deltas are increasingly vulnerable to coastal hazards as declining sediment supply and climate change alter their sediment budget, affecting delta morphology and possibly leading to erosion(1-3). However, the relationship between deltaic sediment budgets, oceanographic forces of waves and tides, and delta morphology has remained poorly quantified. Here we show how the morphology of about 11,000 coastal deltas worldwide, ranging from small bayhead deltas to mega-deltas, has been affected by river damming and deforestation. We introduce a model that shows that present-day delta morphology varies across a continuum between wave (about 80 per cent), tide (around 10 per cent) and river (about 10 per cent) dominance, but that most large deltas are tide- and river-dominated. Over the past 30 years, despite sea-level rise, deltas globally have experienced a net land gain of 54 +/- 12 square kilometres per year (2 standard deviations), with the largest 1 per cent of deltas being responsible for 30 per cent of all net land area gains. Humans are a considerable driver of these net land gains-25 per cent of delta growth can be attributed to deforestation-induced increases in fluvial sediment supply. Yet for nearly 1,000 deltas, river damming(4) has resulted in a severe (more than 50 per cent) reduction in anthropogenic sediment flux, forcing a collective loss of 12 +/- 3.5 square kilometres per year (2 standard deviations) of deltaic land. Not all deltas lose land in response to river damming: deltas transitioning towards tide dominance are currently gaining land, probably through channel infilling. With expected accelerated sea-level rise(5), however, recent land gains are unlikely to be sustained throughout the twenty-first century. Understanding the redistribution of sediments by waves and tides will be critical for successfully predicting human-driven change to deltas, both locally and globally.


A global study of river deltas shows a net increase in delta area by about 54 km(2) yr(-1) over the past 30 years, in part due to deforestation-induced sediment delivery increase.


  
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:36/0  |  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.


  
Floodplain Land Cover and Flow Hydrodynamic Control of Overbank Sedimentation in Compound Channel Flows 期刊论文
WATER RESOURCES RESEARCH, 2019
作者:  Juez, Carmelo;  Schaerer, C.;  Jenny, H.;  Schleiss, A. J.;  Franca, M. J.
收藏  |  浏览/下载:6/0  |  提交时间:2020/02/16
compound channel  floodplain sedimentation  floodplain vegetation  fine sediments  suspended sediment transport  
Simulating rewetting events in intermittent rivers and ephemeral streams: A global analysis of leached nutrients and organic matter 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (5) : 1591-1611
作者:  Shumilova, Oleksandra;  Zak, Dominik;  Datry, Thibault;  von Schiller, Daniel;  Corti, Roland;  Foulquier, Arnaud;  Obrador, Biel;  Tockner, Klement;  Allan, Daniel C.;  Altermatt, Florian;  Isabel Arce, Maria;  Arnon, Shai;  Banas, Damien;  Banegas-Medina, Andy;  Beller, Erin;  Blanchette, Melanie L.;  Blanco-Libreros, Juan F.;  Blessing, Joanna;  Boechat, Iola Goncalves;  Boersma, Kate;  Bogan, Michael T.;  Bonada, Nuria;  Bond, Nick R.;  Brintrup, Kate;  Bruder, Andreas;  Burrows, Ryan;  Cancellario, Tommaso;  Carlson, Stephanie M.;  Cauvy-Fraunie, Sophie;  Cid, Nuria;  Danger, Michael;  de Freitas Terra, Bianca;  De Girolamo, Anna Maria;  del Campo, Ruben;  Dyer, Fiona;  Elosegi, Arturo;  Faye, Emile;  Febria, Catherine;  Figueroa, Ricardo;  Four, Brian;  Gessner, Mark O.;  Gnohossou, Pierre;  Cerezo, Rosa Gomez;  Gomez-Gener, Lluis;  Graca, Manuel A. S.;  Guareschi, Simone;  Guecker, Bjoern;  Hwan, Jason L.;  Kubheka, Skhumbuzo;  Langhans, Simone Daniela;  Leigh, Catherine;  Little, Chelsea J.;  Lorenz, Stefan;  Marshall, Jonathan;  McIntosh, Angus;  Mendoza-Lera, Clara;  Meyer, Elisabeth Irmgard;  Milisa, Marko;  Mlambo, Musa C.;  Moleon, Marcos;  Negus, Peter;  Niyogi, Dev;  Papatheodoulou, Athina;  Pardo, Isabel;  Paril, Petr;  Pesic, Vladimir;  Rodriguez-Lozano, Pablo;  Rolls, Robert J.;  Sanchez-Montoya, Maria Mar;  Savic, Ana;  Steward, Alisha;  Stubbington, Rachel;  Taleb, Amina;  Vander Vorste, Ross;  Waltham, Nathan;  Zoppini, Annamaria;  Zarfl, Christiane
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/26
biofilms  leaching  leaf litter  rewetting  sediments  temporary rivers  
Mobility and Bioavailability of Sediment Phosphorus in Urban Stormwater Ponds 期刊论文
WATER RESOURCES RESEARCH, 2019, 55 (5) : 3680-3688
作者:  Frost, Paul C.;  Prater, Clay;  Scott, Andrew B.;  Song, Keunyea;  Xenopoulos, Marguerite A.
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/26
dissolved organic phosphorus  stormwater management ponds  sediments  phosphorus uptake  retention efficiency  urban ecosystems  
Human and climate global-scale imprint on sediment transfer during the Holocene 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (46) : 22972-22976
作者:  Jean-Philippe Jenny;  Sujan Koirala;  Irene Gregory-Eaves;  Pierre Francus;  Christoph Niemann;  Bernhard Ahrens;  Victor Brovkin;  Alexandre Baud;  Antti E. K. Ojala;  Alexandre Normandeau;  Bernd Zolitschka;  and Nuno Carvalhais
收藏  |  浏览/下载:8/0  |  提交时间:2019/11/27
global soil erosion  lake records  C ages  pollens  varved sediments  
Feasting on terrestrial organic matter: Dining in a dark lake changes microbial decomposition 期刊论文
GLOBAL CHANGE BIOLOGY, 2018, 24 (11) : 5110-5122
作者:  Fitch, Amelia;  Orland, Chloe;  Willer, David;  Emilson, Erik J. S.;  Tanentzap, Andrew J.
收藏  |  浏览/下载:9/0  |  提交时间:2019/04/09
bacterial production  boreal  carbon cycling  enzyme activity  lake sediments  photo-oxidation  
Recycled ancient ghost carbonate in the Pitcairn mantle plume 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (35) : 8682-8687
作者:  Wang, Xiao-Jun;  Chen, Li-Hui;  Hofmann, Albrecht W.;  Hanyu, Takeshi;  Kawabata, Hiroshi;  Zhong, Yuan;  Xie, Lie-Wen;  Shi, Jin-Hua;  Miyazaki, Takashi;  Hirahara, Yuka;  Takahashi, Toshiro;  Senda, Ryoko;  Chang, Qing;  Vaglarov, Bogdan S.;  Kimura, Jun-Ichi
收藏  |  浏览/下载:11/0  |  提交时间:2019/11/27
Pitcairn mantle plume  EM1  magnesium isotopes  ancient carbonate-bearing sediments  
Constructed soils for mitigating lead (Pb) exposure and promoting urban community gardening: The New York City Clean Soil Bank pilot study 期刊论文
LANDSCAPE AND URBAN PLANNING, 2018, 175: 184-194
作者:  Egendorf, Sara Perl;  Cheng, Zhongqi;  Deeb, Maha;  Flores, Victor;  Paltseva, Anna;  Walsh, Daniel;  Groffman, Peter;  Mielke, Howard W.
收藏  |  浏览/下载:4/0  |  提交时间:2019/04/09
Compost  Contamination  Glacial sediments  Manufactured soil  Technosol  Urban agriculture