Metabolic network analysis reveals microbial community interactions in anammox granules.

Abstract:

:Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions. We find that Chlorobi-affiliated bacteria may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate to nitrite. Other heterotrophs may also contribute to scavenging of detritus and peptides produced by anammox bacteria, and potentially use alternative electron donors, such as H2, acetate and formate. Our findings improve the understanding of metabolic activities and interactions between anammox and heterotrophic bacteria and offer the first transcriptional insights on ecosystem function in anammox granules.

journal_name

Nat Commun

journal_title

Nature communications

authors

Lawson CE,Wu S,Bhattacharjee AS,Hamilton JJ,McMahon KD,Goel R,Noguera DR

doi

10.1038/ncomms15416

subject

Has Abstract

pub_date

2017-05-31 00:00:00

pages

15416

issn

2041-1723

pii

ncomms15416

journal_volume

8

pub_type

杂志文章
  • Complementation between polymerase- and exonuclease-deficient mitochondrial DNA polymerase mutants in genomically engineered flies.

    abstract::Replication errors are the main cause of mitochondrial DNA (mtDNA) mutations and a compelling approach to decrease mutation levels would therefore be to increase the fidelity of the catalytic subunit (POLγA) of the mtDNA polymerase. Here we genomically engineer the tamas locus, encoding fly POLγA, and introduce allele...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9808

    authors: Bratic A,Kauppila TE,Macao B,Grönke S,Siibak T,Stewart JB,Baggio F,Dols J,Partridge L,Falkenberg M,Wredenberg A,Larsson NG

    更新日期:2015-11-10 00:00:00

  • Global pattern for the effect of climate and land cover on water yield.

    abstract::Research results on the effects of land cover change on water resources vary greatly and the topic remains controversial. Here we use published data worldwide to examine the validity of Fuh's equation, which relates annual water yield (R) to a wetness index (precipitation/potential evapotranspiration; P/PET) and water...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6918

    authors: Zhou G,Wei X,Chen X,Zhou P,Liu X,Xiao Y,Sun G,Scott DF,Zhou S,Han L,Su Y

    更新日期:2015-01-09 00:00:00

  • Electron tunneling at the molecularly thin 2D perovskite and graphene van der Waals interface.

    abstract::Quasi-two-dimensional perovskites have emerged as a new material platform for optoelectronics on account of its intrinsic stability. A major bottleneck to device performance is the high charge injection barrier caused by organic molecular layers on its basal plane, thus the best performing device currently relies on e...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19331-6

    authors: Leng K,Wang L,Shao Y,Abdelwahab I,Grinblat G,Verzhbitskiy I,Li R,Cai Y,Chi X,Fu W,Song P,Rusydi A,Eda G,Maier SA,Loh KP

    更新日期:2020-10-30 00:00:00

  • Chemical vapour deposition growth of large single crystals of monolayer and bilayer graphene.

    abstract::The growth of large-domain single crystalline graphene with the controllable number of layers is of central importance for large-scale integration of graphene devices. Here we report a new pathway to greatly reduce the graphene nucleation density from ~10(6) to 4 nuclei cm(-2), enabling the growth of giant single crys...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3096

    authors: Zhou H,Yu WJ,Liu L,Cheng R,Chen Y,Huang X,Liu Y,Wang Y,Huang Y,Duan X

    更新日期:2013-01-01 00:00:00

  • Control of Treg cell homeostasis and immune equilibrium by Lkb1 in dendritic cells.

    abstract::To balance immunity and tolerance, the endogenous pool of Foxp3+ regulatory T (Treg) cells is tightly controlled, but the underlying mechanisms of this control remain poorly understood. Here we show that the number of Treg cells is negatively regulated by the kinase Lkb1 in dendritic cells (DCs). Conditional knockout ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07545-8

    authors: Chen S,Fang L,Guo W,Zhou Y,Yu G,Li W,Dong K,Liu J,Luo Y,Wang B,Li Z,Zhao C,Sun Z,Shen Y,Leng Q,Zhou D,Han Z,Huang H,Ren H,Xu G,Feng X

    更新日期:2018-12-13 00:00:00

  • Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis.

    abstract::ASXL1 mutations occur frequently in myeloid neoplasms and are associated with poor prognosis. However, the mechanisms by which mutant ASXL1 induces leukaemogenesis remain unclear. In this study, we report mutually reinforcing effects between a C-terminally truncated form of mutant ASXL1 (ASXL1-MT) and BAP1 in promotin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05085-9

    authors: Asada S,Goyama S,Inoue D,Shikata S,Takeda R,Fukushima T,Yonezawa T,Fujino T,Hayashi Y,Kawabata KC,Fukuyama T,Tanaka Y,Yokoyama A,Yamazaki S,Kozuka-Hata H,Oyama M,Kojima S,Kawazu M,Mano H,Kitamura T

    更新日期:2018-07-16 00:00:00

  • Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa.

    abstract::Fusion proteins containing blue-light-activable protein domains possess great potential as molecular switches in cell signalling. This has recently been impressively demonstrated by connecting the light oxygen voltage LOV2-Jα-protein domain of A. sativa (AsLOV2-Jα) with the Rac1-GTPase, responsible for regulating the ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1121

    authors: Peter E,Dick B,Baeurle SA

    更新日期:2010-11-16 00:00:00

  • Molecular switches from benzene derivatives adsorbed on metal surfaces.

    abstract::Transient precursor states are often experimentally observed for molecules adsorbing on surfaces. However, such precursor states are typically rather short-lived, quickly yielding to more stable adsorption configurations. Here we employ first-principles calculations to systematically explore the interaction mechanism ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3569

    authors: Liu W,Filimonov SN,Carrasco J,Tkatchenko A

    更新日期:2013-01-01 00:00:00

  • Prefrontal attentional saccades explore space rhythmically.

    abstract::Recent studies suggest that attention samples space rhythmically through oscillatory interactions in the frontoparietal network. How these attentional fluctuations coincide with spatial exploration/displacement and exploitation/selection by a dynamic attentional spotlight under top-down control is unclear. Here, we sh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-14649-7

    authors: Gaillard C,Ben Hadj Hassen S,Di Bello F,Bihan-Poudec Y,VanRullen R,Ben Hamed S

    更新日期:2020-02-17 00:00:00

  • Materials genomics methods for high-throughput construction of COFs and targeted synthesis.

    abstract::Materials genomics represents a research mode for materials development, for which reliable methods for efficient materials construction are essential. Here we present a methodology for high-throughput construction of covalent organic frameworks (COFs) based on materials genomics strategy, in which a gene partition me...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07720-x

    authors: Lan Y,Han X,Tong M,Huang H,Yang Q,Liu D,Zhao X,Zhong C

    更新日期:2018-12-10 00:00:00

  • Uncovering the spatial structure of mobility networks.

    abstract::The extraction of a clear and simple footprint of the structure of large, weighted and directed networks is a general problem that has relevance for many applications. An important example is seen in origin-destination matrices, which contain the complete information on commuting flows, but are difficult to analyze an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7007

    authors: Louail T,Lenormand M,Picornell M,García Cantú O,Herranz R,Frias-Martinez E,Ramasco JJ,Barthelemy M

    更新日期:2015-01-21 00:00:00

  • Shaping metallic glasses by electromagnetic pulsing.

    abstract::With damage tolerance rivalling advanced engineering alloys and thermoplastic forming capabilities analogous to conventional plastics, metallic glasses are emerging as a modern engineering material. Here, we take advantage of their unique electrical and rheological properties along with the classic Lorentz force conce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10576

    authors: Kaltenboeck G,Demetriou MD,Roberts S,Johnson WL

    更新日期:2016-02-08 00:00:00

  • Assessment of corneal substrate biomechanics and its effect on epithelial stem cell maintenance and differentiation.

    abstract::Whilst demonstrated extensively in vitro, the control of cell behaviour via modulation of substrate compliance in live tissues has not been accomplished to date. Here we propose that stem cells can be regulated solely through in situ modulation of tissue biomechanics. By first establishing, via high-resolution Brillou...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09331-6

    authors: Gouveia RM,Lepert G,Gupta S,Mohan RR,Paterson C,Connon CJ

    更新日期:2019-04-03 00:00:00

  • A high-stringency blueprint of the human proteome.

    abstract::The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, dev...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/s41467-020-19045-9

    authors: Adhikari S,Nice EC,Deutsch EW,Lane L,Omenn GS,Pennington SR,Paik YK,Overall CM,Corrales FJ,Cristea IM,Van Eyk JE,Uhlén M,Lindskog C,Chan DW,Bairoch A,Waddington JC,Justice JL,LaBaer J,Rodriguez H,He F,Kostrzewa M

    更新日期:2020-10-16 00:00:00

  • CSN6 drives carcinogenesis by positively regulating Myc stability.

    abstract::Cullin-RING ubiquitin ligases (CRLs) are critical in ubiquitinating Myc, while COP9 signalosome (CSN) controls neddylation of Cullin in CRL. The mechanistic link between Cullin neddylation and Myc ubiquitination/degradation is unclear. Here we show that Myc is a target of the CSN subunit 6 (CSN6)-Cullin signalling axi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6384

    authors: Chen J,Shin JH,Zhao R,Phan L,Wang H,Xue Y,Post SM,Ho Choi H,Chen JS,Wang E,Zhou Z,Tseng C,Gully C,Velazquez-Torres G,Fuentes-Mattei E,Yeung G,Qiao Y,Chou PC,Su CH,Hsieh YC,Hsu SL,Ohshiro K,Shaikenov T,Wang H

    更新日期:2014-11-14 00:00:00

  • The shift of phosphorus transfers in global fisheries and aquaculture.

    abstract::Global fish production (capture and aquaculture) has increased quickly, which has altered global flows of phosphorus (P). Here we show that in 2016, [Formula: see text] Tg P yr-1 (mean and interquartile range) was applied in aquaculture to increase fish production; while [Formula: see text] Tg P yr-1 was removed from ...

    journal_title:Nature communications

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41467-019-14242-7

    authors: Huang Y,Ciais P,Goll DS,Sardans J,Peñuelas J,Cresto-Aleina F,Zhang H

    更新日期:2020-01-17 00:00:00

  • miR-23b and miR-218 silencing increase Muscleblind-like expression and alleviate myotonic dystrophy phenotypes in mammalian models.

    abstract::Functional depletion of the alternative splicing factors Muscleblind-like (MBNL 1 and 2) is at the basis of the neuromuscular disease myotonic dystrophy type 1 (DM1). We previously showed the efficacy of miRNA downregulation in Drosophila DM1 model. Here, we screen for miRNAs that regulate MBNL1 and MBNL2 in HeLa cell...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04892-4

    authors: Cerro-Herreros E,Sabater-Arcis M,Fernandez-Costa JM,Moreno N,Perez-Alonso M,Llamusi B,Artero R

    更新日期:2018-06-26 00:00:00

  • Cellular microRNA networks regulate host dependency of hepatitis C virus infection.

    abstract::Cellular microRNAs (miRNAs) have been shown to regulate hepatitis C virus (HCV) replication, yet a systematic interrogation of the repertoire of miRNAs impacting HCV life cycle is lacking. Here we apply integrative functional genomics strategies to elucidate global HCV-miRNA interactions. Through genome-wide miRNA mim...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01954-x

    authors: Li Q,Lowey B,Sodroski C,Krishnamurthy S,Alao H,Cha H,Chiu S,El-Diwany R,Ghany MG,Liang TJ

    更新日期:2017-11-27 00:00:00

  • Dietary diversity and evolution of the earliest flying vertebrates revealed by dental microwear texture analysis.

    abstract::Pterosaurs, the first vertebrates to evolve active flight, lived between 210 and 66 million years ago. They were important components of Mesozoic ecosystems, and reconstructing pterosaur diets is vital for understanding their origins, their roles within Mesozoic food webs and the impact of other flying vertebrates (i....

    journal_title:Nature communications

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41467-020-19022-2

    authors: Bestwick J,Unwin DM,Butler RJ,Purnell MA

    更新日期:2020-10-28 00:00:00

  • An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production.

    abstract::Ionic liquids (ILs) are emerging as superior solvents for numerous industrial applications, including the pretreatment of biomass for the microbial production of biofuels. However, some of the most effective ILs used to solubilize cellulose inhibit microbial growth, decreasing efficiency in the overall process. Here w...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4490

    authors: Ruegg TL,Kim EM,Simmons BA,Keasling JD,Singer SW,Lee TS,Thelen MP

    更新日期:2014-03-26 00:00:00

  • Astrocytic laminin regulates pericyte differentiation and maintains blood brain barrier integrity.

    abstract::Blood brain barrier (BBB) breakdown is not only a consequence of but also contributes to many neurological disorders, including stroke and Alzheimer's disease. How the basement membrane (BM) contributes to the normal functioning of the BBB remains elusive. Here we use conditional knockout mice and an acute adenovirus-...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4413

    authors: Yao Y,Chen ZL,Norris EH,Strickland S

    更新日期:2014-03-03 00:00:00

  • PRKAA1/AMPKα1-driven glycolysis in endothelial cells exposed to disturbed flow protects against atherosclerosis.

    abstract::Increased aerobic glycolysis in endothelial cells of atheroprone areas of blood vessels has been hypothesized to drive increased inflammation and lesion burden but direct links remain to be established. Here we show that endothelial cells exposed to disturbed flow in vivo and in vitro exhibit increased levels of prote...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07132-x

    authors: Yang Q,Xu J,Ma Q,Liu Z,Sudhahar V,Cao Y,Wang L,Zeng X,Zhou Y,Zhang M,Xu Y,Wang Y,Weintraub NL,Zhang C,Fukai T,Wu C,Huang L,Han Z,Wang T,Fulton DJ,Hong M,Huo Y

    更新日期:2018-11-07 00:00:00

  • Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.

    abstract::Knowledge of cell type composition in disease relevant tissues is an important step towards the identification of cellular targets of disease. We present MuSiC, a method that utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-08023-x

    authors: Wang X,Park J,Susztak K,Zhang NR,Li M

    更新日期:2019-01-22 00:00:00

  • Direct observation of desorption of a melt of long polymer chains.

    abstract::Tuning the thermodynamic state of a material has a tremendous impact on its performance. In the case of polymers placed in proximity of a solid wall, this is possible by annealing above the glass transition temperature, Tg, which induces the formation of an adsorbed layer. Whether heating to higher temperatures would ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18216-y

    authors: Monnier X,Napolitano S,Cangialosi D

    更新日期:2020-08-28 00:00:00

  • Attosecond interferometry with self-amplified spontaneous emission of a free-electron laser.

    abstract::Light-phase-sensitive techniques, such as coherent multidimensional spectroscopy, are well-established in a broad spectral range, already spanning from radio-frequencies in nuclear magnetic resonance spectroscopy to visible and ultraviolet wavelengths in nonlinear optics with table-top lasers. In these cases, the abil...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15626

    authors: Usenko S,Przystawik A,Jakob MA,Lazzarino LL,Brenner G,Toleikis S,Haunhorst C,Kip D,Laarmann T

    更新日期:2017-05-30 00:00:00

  • Surface plasmon resonance extension through two-block metal-conducting polymer nanorods.

    abstract::Research on surface plasmon resonance coupling of metallic nanostructures is an important area in the field of plasmonics because distinctive collective optical properties can be realized that are different from the individual constituents. Here we report the localized surface plasmon resonance of hybrid metal-organic...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03453-z

    authors: Jung I,Kim M,Kwak M,Kim G,Jang M,Kim SM,Park DJ,Park S

    更新日期:2018-03-08 00:00:00

  • Downstream changes in river avulsion style are related to channel morphology.

    abstract::One of the most dramatic events in river environments is the natural diversion, or avulsion, of a channel across its floodplain. Though rarely witnessed, avulsions can cause massive floods, and over geologic time they create most of the fluvial stratigraphic record. Avulsions exhibit behavior ranging from reoccupying ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15859-9

    authors: Valenza JM,Edmonds DA,Hwang T,Roy S

    更新日期:2020-04-30 00:00:00

  • Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells.

    abstract::Precise rare-cell technologies require the blood to be processed immediately or be stabilized with fixatives. Such restrictions limit the translation of circulating tumor cell (CTC)-based liquid biopsy assays that provide accurate molecular data in guiding clinical decisions. Here we describe a method to preserve whol...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01705-y

    authors: Wong KHK,Tessier SN,Miyamoto DT,Miller KL,Bookstaver LD,Carey TR,Stannard CJ,Thapar V,Tai EC,Vo KD,Emmons ES,Pleskow HM,Sandlin RD,Sequist LV,Ting DT,Haber DA,Maheswaran S,Stott SL,Toner M

    更新日期:2017-11-23 00:00:00

  • Extreme-ultraviolet high-harmonic generation in liquids.

    abstract::High-harmonic generation (HHG) in gases has been the main enabling technology of attosecond science since its discovery. Recently, HHG from solids has been demonstrated, opening a lively area of research. In contrast, harmonic generation from liquids has so far remained restricted to low harmonics in the visible regim...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06040-4

    authors: Luu TT,Yin Z,Jain A,Gaumnitz T,Pertot Y,Ma J,Wörner HJ

    更新日期:2018-09-13 00:00:00

  • Towards a new approach to reveal dynamical organization of the brain using topological data analysis.

    abstract::Little is known about how our brains dynamically adapt for efficient functioning. Most previous work has focused on analyzing changes in co-fluctuations between a set of brain regions over several temporal segments of the data. We argue that by collapsing data in space or time, we stand to lose useful information abou...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03664-4

    authors: Saggar M,Sporns O,Gonzalez-Castillo J,Bandettini PA,Carlsson G,Glover G,Reiss AL

    更新日期:2018-04-11 00:00:00