当前期刊: The ISME Journal Go to current issue    加入关注   
显示样式:        排序: IF: - GO 导出
我的关注
我的收藏
您暂时未登录!
登录
  • Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Héloïse Rouzé; Pierre E. Galand; Mónica Medina; Pim Bongaerts; Michel Pichon; Gonzalo Pérez-Rosales; Gergely Torda; Aurelie Moya; Jean-Baptiste Raina; Laetitia Hédouin

    The symbiosis between scleractinian corals and photosynthetic algae from the family Symbiodiniaceae underpins the health and productivity of tropical coral reef ecosystems. While this photosymbiotic association has been extensively studied in shallow waters (<30 m depth), we do not know how deeper corals, inhabiting large and vastly underexplored mesophotic coral ecosystems, modulate their symbiotic

    更新日期:2021-01-16
  • Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Jiahao Gu; Xiaojun Wang; Xiaopan Ma; Ying Sun; Xiang Xiao; Haiwei Luo

    Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis

    更新日期:2021-01-16
  • Acclimation and adaptation to elevated p CO 2 increase arsenic resilience in marine diatoms
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Dong Xu; Charlotte-Elisa Schaum; Bin Li; Yanan Chen; Shanying Tong; Fei-Xue Fu; David A. Hutchins; Xiaowen Zhang; Xiao Fan; Wentao Han; Yitao Wang; Naihao Ye

    Arsenic pollution is a widespread threat to marine life, but the ongoing rise pCO2 levels is predicted to decrease bio-toxicity of arsenic. However, the effects of arsenic toxicity on marine primary producers under elevated pCO2 are not well characterized. Here, we studied the effects of arsenic toxicity in three globally distributed diatom species (Phaeodactylum tricornutum, Thalassiosira pseudonana

    更新日期:2021-01-16
  • Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Chloé M. J. Baumas; Frédéric A. C. Le Moigne; Marc Garel; Nagib Bhairy; Sophie Guasco; Virginie Riou; Fabrice Armougom; Hans-Peter Grossart; Christian Tamburini

    The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological

    更新日期:2021-01-16
  • Comparative genomics reveals new functional insights in uncultured MAST species
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Aurelie Labarre; David López-Escardó; Francisco Latorre; Guy Leonard; François Bucchini; Aleix Obiol; Corinne Cruaud; Michael E. Sieracki; Olivier Jaillon; Patrick Wincker; Klaas Vandepoele; Ramiro Logares; Ramon Massana

    Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to

    更新日期:2021-01-16
  • Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Jia-Wei Zhang; Hong-Po Dong; Li-Jun Hou; Yang Liu; Ya-Fei Ou; Yan-Ling Zheng; Ping Han; Xia Liang; Guo-Yu Yin; Dian-Ming Wu; Min Liu; Meng Li

    Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota

    更新日期:2021-01-16
  • Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter -like endosymbiont that possesses multiple putative toxin-antitoxin systems
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Samriti Midha; Daniel J. Rigden; Stefanos Siozios; Gregory D. D. Hurst; Andrew P. Jackson

    Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that

    更新日期:2021-01-16
  • Novel dichloromethane-fermenting bacteria in the Peptococcaceae family
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Sophie I. Holland; Haluk Ertan; Kate Montgomery; Michael J. Manefield; Matthew Lee

    Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism

    更新日期:2021-01-16
  • Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Qing Liu; Wei Li; Di Liu; Lingyan Li; Jie Li; Na Lv; Fei Liu; Baoli Zhu; Yuguang Zhou; Yuhua Xin; Xiuzhu Dong

    Bacteria that inhabit glaciers usually produce carotenoids. Here, we report that a group of zeaxanthin-producing glacial Flavobacterium exhibited light-promoted growth. Of the tested 47 strains, 45 showed increased growths but two died under illumination at 50 μmol photon m−2 s−1. Light stimulation occurred mainly in either anoxic or nutrient-poor cultures, while the same levels of light promotion

    更新日期:2021-01-16
  • Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Maureen Berg; Danielle Goudeau; Charles Olmsted; Katherine D. McMahon; Senay Yitbarek; Jennifer L. Thweatt; Donald A. Bryant; Emiley A. Eloe-Fadrosh; Rex R. Malmstrom; Simon Roux

    Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes

    更新日期:2021-01-16
  • Environmental stress destabilizes microbial networks
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Damian J. Hernandez; Aaron S. David; Eric S. Menges; Christopher A. Searcy; Michelle E. Afkhami

    Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil

    更新日期:2021-01-16
  • Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
    ISME J. (IF 9.18) Pub Date : 2021-01-15
    Anik Dutta; Fanny E. Hartmann; Carolina Sardinha Francisco; Bruce A. McDonald; Daniel Croll

    The adaptive potential of pathogens in novel or heterogeneous environments underpins the risk of disease epidemics. Antagonistic pleiotropy or differential resource allocation among life-history traits can constrain pathogen adaptation. However, we lack understanding of how the genetic architecture of individual traits can generate trade-offs. Here, we report a large-scale study based on 145 global

    更新日期:2021-01-16
  • Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
    ISME J. (IF 9.18) Pub Date : 2021-01-11
    Sundy Maurice; Gontran Arnault; Jenni Nordén; Synnøve Smebye Botnen; Otto Miettinen; Håvard Kauserud

    Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic

    更新日期:2021-01-12
  • Constrained proteome allocation affects coexistence in models of competitive microbial communities
    ISME J. (IF 9.18) Pub Date : 2021-01-11
    Leonardo Pacciani-Mori; Samir Suweis; Amos Maritan; Andrea Giometto

    Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the structure and composition of microbial communities are intertwined with the metabolism of the species

    更新日期:2021-01-12
  • Pantothenate mediates the coordination of whitefly and symbiont fitness
    ISME J. (IF 9.18) Pub Date : 2021-01-11
    Fei-Rong Ren; Xiang Sun; Tian-Yu Wang; Jin-Yang Yan; Ya-Lin Yao; Chu-Qiao Li; Jun-Bo Luan

    Intracellular symbionts in insects often have reduced genomes. Host acquisition of genes from bacteria is an important adaptation that supports symbionts. However, the function of horizontally transferred genes in insect symbiosis remains largely unclear. The primary symbiont Portiera housed in bacteriocytes lacks pantothenate synthesis genes: panB and panC, which is presumably complemented by a fused

    更新日期:2021-01-12
  • Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress
    ISME J. (IF 9.18) Pub Date : 2021-01-11
    Pablo I. Nikel; Tobias Fuhrer; Max Chavarría; Alberto Sánchez-Pascuala; Uwe Sauer; Víctor de Lorenzo

    As a frequent inhabitant of sites polluted with toxic chemicals, the soil bacterium and plant-root colonizer Pseudomonas putida can tolerate high levels of endogenous and exogenous oxidative stress. Yet, the ultimate reason of such phenotypic property remains largely unknown. To shed light on this question, metabolic network-wide routes for NADPH generation—the metabolic currency that fuels redox-stress

    更新日期:2021-01-12
  • Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas
    ISME J. (IF 9.18) Pub Date : 2021-01-08
    Justin A. Meeds; J. Marty Kranabetter; Ieva Zigg; Dave Dunn; François Miros; Paul Shipley; Melanie D. Jones

    Ectomycorrhizal (EM) fungi can acquire phosphorus (P) through the production of extracellular hydrolytic enzymes (exoenzymes), but it is unclear as to the manner and extent native EM fungal communities respond to declining soil P availability. We examined the activity of six exoenzymes (xylosidase, N-acetyl glucosaminidase, β-glucosidase, acid phosphomonoesterase, acid phosphodiesterase [APD], laccase)

    更新日期:2021-01-08
  • Functional mutants of Azospirillum brasilense elicit beneficial physiological and metabolic responses in Zea mays contributing to increased host iron assimilation
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    A. B. Housh; G. Powell; S. Scott; A. Anstaett; A. Gerheart; M. Benoit; S. Waller; A. Powell; J. M. Guthrie; B. Higgins; S. L. Wilder; M. J. Schueller; R. A. Ferrieri

    Iron (Fe), an essential element for plant growth, is abundant in soil but with low bioavailability. Thus, plants developed specialized mechanisms to sequester the element. Beneficial microbes have recently become a favored method to promote plant growth through increased uptake of essential micronutrients, like Fe, yet little is known of their mechanisms of action. Functional mutants of the epiphytic

    更新日期:2021-01-07
  • Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    Xin Sun; Claudia Frey; Emilio Garcia-Robledo; Amal Jayakumar; Bess B. Ward

    Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic

    更新日期:2021-01-07
  • Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    Zhongtao Zhao; Xiaojuan Li; Ming Fai Liu; Vincent S. F. T. Merckx; Richard M. K. Saunders; Dianxiang Zhang

    Mycoheterotrophic plants (MHPs) growing on arbuscular mycorrhizal fungi (AMF) usually maintain specialized mycorrhizal associations. The level of specificity varies between MHPs, although it remains largely unknown whether interactions with mycorrhizal fungi differ by plant lineage, species, and/or by population. Here, we investigate the mycorrhizal interactions among Burmannia species (Burmanniaceae)

    更新日期:2021-01-07
  • Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    Annelein Meisner; Basten L. Snoek; Joseph Nesme; Elizabeth Dent; Samuel Jacquiod; Aimée T. Classen; Anders Priemé

    Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response

    更新日期:2021-01-07
  • Cervicovaginal bacterial communities in reproductive-aged Tanzanian women with Schistosoma mansoni , Schistosoma haematobium , or without schistosome infection
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    Brooke W. Bullington; Myung Hee Lee; Jane Mlingi; Ndalloh Paul; Christine Aristide; Emily Fontana; Eric R. Littmann; Crispin Mukerebe; Peter Shigella; Philibert Kashangaki; Samuel E. Kalluvya; Claudia J. de Dood; Govert J. van Dam; Paul L.A.M. Corstjens; Daniel W. Fitzgerald; Eric G. Pamer; Jennifer A. Downs

    Schistosome infection is recognized as a potentially modifiable risk factor for HIV in women by the World Health Organization. Alterations in cervicovaginal bacteria have been associated with HIV acquisition and have not been studied in schistosome infection. We collected cervical swabs from Tanzanian women with and without S. mansoni and S. haematobium to determine effects on cervicovaginal microbiota

    更新日期:2021-01-07
  • Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
    ISME J. (IF 9.18) Pub Date : 2021-01-06
    Gabrielle L. Harrow; John A. Lees; William P. Hanage; Marc Lipsitch; Jukka Corander; Caroline Colijn; Nicholas J. Croucher

    Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium

    更新日期:2021-01-06
  • A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen
    ISME J. (IF 9.18) Pub Date : 2020-12-28
    Anilei Hoare; Hui Wang; Archana Meethil; Loreto Abusleme; Bo-Young Hong; Niki M. Moutsopoulos; Philip D. Marsh; George Hajishengallis; Patricia I. Diaz

    Recent studies describe in detail the shifts in composition of human-associated polymicrobial communities from health to disease. However, the specific processes that drive the colonization and overgrowth of pathogens within these communities remain incompletely understood. We used in vitro culture systems and a disease-relevant mouse model to show that population size, which determines the availability

    更新日期:2020-12-28
  • Microbial N 2 O consumption in and above marine N 2 O production hotspots
    ISME J. (IF 9.18) Pub Date : 2020-12-21
    Xin Sun; Amal Jayakumar; John C. Tracey; Elizabeth Wallace; Colette L. Kelly; Karen L. Casciotti; Bess B. Ward

    The ocean is a net source of N2O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N2O via microbial N2O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand N2O consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic

    更新日期:2020-12-21
  • CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa
    ISME J. (IF 9.18) Pub Date : 2020-12-21
    Rachel M. Wheatley; R. Craig MacLean

    CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas

    更新日期:2020-12-21
  • Morphological complexity affects the diversity of marine microbiomes
    ISME J. (IF 9.18) Pub Date : 2020-12-21
    Matthew A. Lemay; Melissa Y. Chen; Florent Mazel; Katharine R. Hind; Samuel Starko; Patrick J. Keeling; Patrick T. Martone; Laura Wegener Parfrey

    Large eukaryotes support diverse communities of microbes on their surface—epibiota—that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity—host evolutionary history and ecology, environmental conditions and stochasticity—do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from

    更新日期:2020-12-21
  • Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps
    ISME J. (IF 9.18) Pub Date : 2020-12-20
    Tomeu Viver; Roth E. Conrad; Luis H. Orellana; Mercedes Urdiain; José E. González-Pastor; Janet K. Hatt; Rudolf Amann; Josefa Antón; Konstantinos T. Konstantinidis; Ramon Rosselló-Móra

    Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts

    更新日期:2020-12-21
  • Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals
    ISME J. (IF 9.18) Pub Date : 2020-12-20
    Andrew R. Babbin; Tyler Tamasi; Diana Dumit; Laura Weber; María Victoria Iglesias Rodríguez; Sarah L. Schwartz; Maickel Armenteros; Scott D. Wankel; Amy Apprill

    Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium

    更新日期:2020-12-21
  • Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities
    ISME J. (IF 9.18) Pub Date : 2020-12-20
    Miaoxiao Wang; Xiaonan Liu; Yong Nie; Xiao-Lei Wu

    Microbes release a wide variety of metabolites to the environment that benefit the whole population, called public goods. Public goods sharing drives adaptive function loss, and allows the rise of metabolic cross-feeding. However, how public goods sharing governs the succession of communities over evolutionary time scales remains unclear. To resolve this issue, we constructed an individual-based model

    更新日期:2020-12-21
  • Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation
    ISME J. (IF 9.18) Pub Date : 2020-12-20
    Eric L. Bruger; Daniel J. Synder; Vaughn S. Cooper; Christopher M. Waters

    As selection frequently favors noncooperating defectors in mixed populations with cooperators, mechanisms that promote cooperation stability clearly exist. One potential mechanism is bacterial cell-to-cell communication, quorum sensing (QS), which can allow cooperators to prevent invasion by defectors. However, the impact of QS on widespread maintenance of cooperation in well-mixed conditions has not

    更新日期:2020-12-21
  • Pervasive prophage recombination occurs during evolution of spore-forming Bacilli
    ISME J. (IF 9.18) Pub Date : 2020-12-20
    Anna Dragoš; B. Priyadarshini; Zahraa Hasan; Mikael Lenz Strube; Paul J. Kempen; Gergely Maróti; Charlotte Kaspar; Baundauna Bose; Briana M. Burton; Ilka B. Bischofs; Ákos T. Kovács

    Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population

    更新日期:2020-12-21
  • Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota
    ISME J. (IF 9.18) Pub Date : 2020-12-17
    Kate A. Sabey; Se Jin Song; Anna Jolles; Rob Knight; Vanessa O. Ezenwa

    Changes in the gut microbiota during pathogen infection are often predicted to influence disease outcomes. However, studies exploring whether pathogens induce microbiota shifts have yielded inconsistent results. This suggests that variation in infection, rather than the presence of infection alone, might shape pathogen–microbiota relationships. For example, most hosts are coinfected with multiple pathogens

    更新日期:2020-12-17
  • Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents
    ISME J. (IF 9.18) Pub Date : 2020-12-17
    Sean M. McAllister; Rebecca Vandzura; Jessica L. Keffer; Shawn W. Polson; Clara S. Chan

    In principle, iron oxidation can fuel significant primary productivity and nutrient cycling in dark environments such as the deep sea. However, we have an extremely limited understanding of the ecology of iron-based ecosystems, and thus the linkages between iron oxidation, carbon cycling, and nitrate reduction. Here we investigate iron microbial mats from hydrothermal vents at Lōʻihi Seamount, Hawaiʻi

    更新日期:2020-12-17
  • Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels
    ISME J. (IF 9.18) Pub Date : 2020-12-15
    Mohammad H. Mirhakkak; Sascha Schäuble; Tilman E. Klassert; Sascha Brunke; Philipp Brandt; Daniel Loos; Ruben V. Uribe; Felipe Senne de Oliveira Lino; Yueqiong Ni; Slavena Vylkova; Hortense Slevogt; Bernhard Hube; Glen J. Weiss; Morten O. A. Sommer; Gianni Panagiotou

    Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance. We optimized the predictive capacity of our model using wild type and mutant

    更新日期:2020-12-15
  • Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion
    ISME J. (IF 9.18) Pub Date : 2020-12-15
    Jaime González; Manuel Salvador; Özhan Özkaya; Matt Spick; Kate Reid; Catia Costa; Melanie J. Bailey; Claudio Avignone Rossa; Rolf Kümmerli; José I. Jiménez

    The rapid emergence of antibiotic resistant bacterial pathogens constitutes a critical problem in healthcare and requires the development of novel treatments. Potential strategies include the exploitation of microbial social interactions based on public goods, which are produced at a fitness cost by cooperative microorganisms, but can be exploited by cheaters that do not produce these goods. Cheater

    更新日期:2020-12-15
  • Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium
    ISME J. (IF 9.18) Pub Date : 2020-12-10
    Nunzia Picone; Arjan Pol; Rob Mesman; Maartje A. H. J. van Kessel; Geert Cremers; Antonie H. van Gelder; Theo A. van Alen; Mike S. M. Jetten; Sebastian Lücker; Huub J. M. Op den Camp

    Ammonia oxidation was considered impossible under highly acidic conditions, as the protonation of ammonia leads to decreased substrate availability and formation of toxic nitrogenous compounds. Recently, some studies described archaeal and bacterial ammonia oxidizers growing at pH as low as 4, while environmental studies observed nitrification at even lower pH values. In this work, we report on the

    更新日期:2020-12-10
  • Glycogen metabolism of the anammox bacterium “ Candidatus Brocadia sinica”
    ISME J. (IF 9.18) Pub Date : 2020-12-07
    Satoshi Okabe; Amrini Amalia Shafdar; Kanae Kobayashi; Lei Zhang; Mamoru Oshiki

    Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in “Ca. Brocadia sinica” growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the

    更新日期:2020-12-07
  • Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes ( Ca . Poseidoniales) in the North Western Mediterranean Sea
    ISME J. (IF 9.18) Pub Date : 2020-12-07
    Olivier Pereira; Corentin Hochart; Dominique Boeuf; Jean Christophe Auguet; Didier Debroas; Pierre E. Galand

    The Archaea Marine Group II (MGII) is widespread in the world’s ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group’s metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean

    更新日期:2020-12-07
  • Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community
    ISME J. (IF 9.18) Pub Date : 2020-12-03
    Lauren M. Seyler; Elizabeth Trembath-Reichert; Benjamin J. Tully; Julie A. Huber

    The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic

    更新日期:2020-12-03
  • Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions
    ISME J. (IF 9.18) Pub Date : 2020-12-03
    Igor Grekov; Janne Gesine Thöming; Adrian Kordes; Susanne Häussler

    Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted

    更新日期:2020-12-03
  • Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen
    ISME J. (IF 9.18) Pub Date : 2020-12-01
    Javad Gharechahi; Mohammad Farhad Vahidi; Mohammad Bahram; Jian-Lin Han; Xue-Zhi Ding; Ghasem Hosseini Salekdeh

    Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated

    更新日期:2020-12-01
  • Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation
    ISME J. (IF 9.18) Pub Date : 2020-11-30
    Elizabeth M. Fones; Daniel R. Colman; Emily A. Kraus; Ramunas Stepanauskas; Alexis S. Templeton; John R. Spear; Eric S. Boyd

    Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation

    更新日期:2020-12-01
  • Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation
    ISME J. (IF 9.18) Pub Date : 2020-11-30
    Ian D. E. A. Lidbury; Chiara Borsetto; Andrew R. J. Murphy; Andrew Bottrill; Alexandra M. E. Jones; Gary D. Bending; John P. Hammond; Yin Chen; Elizabeth M. H. Wellington; David J. Scanlan

    Bacteroidetes are abundant pathogen-suppressing members of the plant microbiome that contribute prominently to rhizosphere phosphorus mobilisation, a frequent growth-limiting nutrient in this niche. However, the genetic traits underpinning their success in this niche remain largely unknown, particularly regarding their phosphorus acquisition strategies. By combining cultivation, multi-layered omics

    更新日期:2020-12-01
  • Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum
    ISME J. (IF 9.18) Pub Date : 2020-11-23
    Andreas Altenburger; Huimin Cai; Qiye Li; Kirstine Drumm; Miran Kim; Yuanzhen Zhu; Lydia Garcia-Cuetos; Xiaoyu Zhan; Per Juel Hansen; Uwe John; Shuaicheng Li; Nina Lundholm

    The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey

    更新日期:2020-11-23
  • Ecological drivers switch from bottom–up to top–down during model microbial community successions
    ISME J. (IF 9.18) Pub Date : 2020-11-23
    Sven P. Tobias-Hünefeldt; Jess Wenley; Federico Baltar; Sergio E. Morales

    Bottom–up selection has an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top–down selection (e.g., predation) may be partially responsible for the unexplained variance. However, top–down processes and their interaction with bottom–up selective pressures often remain unexplored. We utilised an in situ marine biofilm model system

    更新日期:2020-11-23
  • Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning
    ISME J. (IF 9.18) Pub Date : 2020-11-23
    Elaina D. Graham; Benjamin J. Tully

    The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available

    更新日期:2020-11-23
  • Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions
    ISME J. (IF 9.18) Pub Date : 2020-11-23
    Barbara Bayer; Mak A. Saito; Matthew R. McIlvin; Sebastian Lücker; Dawn M. Moran; Thomas S. Lankiewicz; Christopher L. Dupont; Alyson E. Santoro

    The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test

    更新日期:2020-11-23
  • Engineering rhizobacteria for sustainable agriculture
    ISME J. (IF 9.18) Pub Date : 2020-11-23
    Timothy L. Haskett; Andrzej Tkacz; Philip S. Poole

    Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic

    更新日期:2020-11-23
  • Ecology and evolution of antimicrobial resistance in bacterial communities
    ISME J. (IF 9.18) Pub Date : 2020-11-20
    Michael J. Bottery; Jonathan W. Pitchford; Ville-Petri Friman

    Accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity to antibiotics. In this perspective, we argue that resistance and evolutionary responses to antibiotic treatments should not be considered only a trait of an individual

    更新日期:2020-11-21
  • Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment
    ISME J. (IF 9.18) Pub Date : 2020-11-18
    Claus Pelikan; Kenneth Wasmund; Clemens Glombitza; Bela Hausmann; Craig W. Herbold; Mathias Flieder; Alexander Loy

    Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria

    更新日期:2020-11-18
  • Elevated CO 2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function
    ISME J. (IF 9.18) Pub Date : 2020-11-18
    Alla Usyskin-Tonne; Yitzhak Hadar; Uri Yermiyahu; Dror Minz

    Elevated CO2 stimulates plant growth and affects quantity and composition of root exudates, followed by response of its microbiome. Three scenarios representing nitrate fertilization regimes: limited (30 ppm), moderate (70 ppm) and excess nitrate (100 ppm) were compared under ambient and elevated CO2 (eCO2, 850 ppm) to elucidate their combined effects on root-surface-associated bacterial community

    更新日期:2020-11-18
  • Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
    ISME J. (IF 9.18) Pub Date : 2020-11-16
    M. Consuelo Gazitúa; Dean R. Vik; Simon Roux; Ann C. Gregory; Benjamin Bolduc; Brittany Widner; Margaret R. Mulholland; Steven J. Hallam; Osvaldo Ulloa; Matthew B. Sullivan

    Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known

    更新日期:2020-11-16
  • Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed
    ISME J. (IF 9.18) Pub Date : 2020-11-13
    Jared Bernard; Christopher B. Wall; Maria S. Costantini; Randi L. Rollins; Melissa L. Atkins; Feresa P. Cabrera; Nicolas D. Cetraro; Christian K. J. Feliciano; Austin L. Greene; Philip K. Kitamura; Alejandro Olmedo-Velarde; Vithanage N. S. Sirimalwatta; Helen W. Sung; Leah P. M. Thompson; Huong T. Vu; Chad J. Wilhite; Anthony S. Amend

    Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across

    更新日期:2020-11-13
  • Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
    ISME J. (IF 9.18) Pub Date : 2020-11-13
    Dimitra Sakoula; Hanna Koch; Jeroen Frank; Mike S. M. Jetten; Maartje A. H. J. van Kessel; Sebastian Lücker

    The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the

    更新日期:2020-11-13
  • Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance
    ISME J. (IF 9.18) Pub Date : 2020-11-11
    Melanie Maria Obermeier; Wisnu Adi Wicaksono; Julian Taffner; Alessandro Bergna; Anja Poehlein; Tomislav Cernava; Stefanie Lindstaedt; Mario Lovric; Christina Andrea Müller Bogotá; Gabriele Berg

    The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library

    更新日期:2020-11-12
  • Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures
    ISME J. (IF 9.18) Pub Date : 2020-11-05
    David A. Aromokeye; Oluwatobi E. Oni; Jan Tebben; Xiuran Yin; Tim Richter-Heitmann; Jenny Wendt; Rolf Nimzyk; Sten Littmann; Daniela Tienken; Ajinkya C. Kulkarni; Susann Henkel; Kai-Uwe Hinrichs; Marcus Elvert; Tilmann Harder; Sabine Kasten; Michael W. Friedrich

    Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance

    更新日期:2020-11-06
  • Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
    ISME J. (IF 9.18) Pub Date : 2020-11-04
    Fabienne Benz; Jana S. Huisman; Erik Bakkeren; Joana A. Herter; Tanja Stadler; Martin Ackermann; Médéric Diard; Adrian Egli; Alex R. Hall; Wolf-Dietrich Hardt; Sebastian Bonhoeffer

    Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics

    更新日期:2020-11-04