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  • 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
  • Skin fungal assemblages of bats vary based on susceptibility to white-nose syndrome
    ISME J. (IF 9.18) Pub Date : 2020-11-04
    Karen J. Vanderwolf; Lewis J. Campbell; Tony L. Goldberg; David S. Blehert; Jeffrey M. Lorch

    Microbial skin assemblages, including fungal communities, can influence host resistance to infectious diseases. The diversity-invasibility hypothesis predicts that high-diversity communities are less easily invaded than species-poor communities, and thus diverse microbial communities may prevent pathogens from colonizing a host. To explore the hypothesis that host fungal communities mediate resistance

    更新日期:2020-11-04
  • Subgroup level differences of physiological activities in marine Lokiarchaeota
    ISME J. (IF 9.18) Pub Date : 2020-11-04
    Xiuran Yin; Mingwei Cai; Yang Liu; Guowei Zhou; Tim Richter-Heitmann; David A. Aromokeye; Ajinkya C. Kulkarni; Rolf Nimzyk; Henrik Cullhed; Zhichao Zhou; Jie Pan; Yuchun Yang; Ji-Dong Gu; Marcus Elvert; Meng Li; Michael W. Friedrich

    Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus ‘Prometheoarchaeum syntrophicum’. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope

    更新日期:2020-11-04
  • Candida albicans promotes tooth decay by inducing oral microbial dysbiosis
    ISME J. (IF 9.18) Pub Date : 2020-11-04
    Qian Du; Biao Ren; Jinzhi He; Xian Peng; Qiang Guo; Liwei Zheng; Jiyao Li; Huanqin Dai; Vivian Chen; Lixin Zhang; Xuedong Zhou; Xin Xu

    Candida albicans has been detected in root carious lesions. The current study aimed to explore the action of this fungal species on the microbial ecology and the pathogenesis of root caries. Here, by analyzing C. albicans in supragingival dental plaque collected from root carious lesions and sound root surfaces of root-caries subjects as well as caries-free individuals, we observed significantly increased

    更新日期:2020-11-04
  • Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
    ISME J. (IF 9.18) Pub Date : 2020-11-02
    Robyn J. Wright; Morgan G. I. Langille; Tony R. Walker

    It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment—termed the “Plastisphere”—may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies

    更新日期:2020-11-02
  • Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment
    ISME J. (IF 9.18) Pub Date : 2020-11-02
    David J. Levy-Booth; Ameena Hashimi; Raphael Roccor; Li-Yang Liu; Scott Renneckar; Lindsay D. Eltis; William W. Mohn

    Thermal swamps are unique ecosystems where geothermally warmed waters mix with decomposing woody biomass, hosting novel biogeochemical-cycling and lignin-degrading microbial consortia. Assembly of shotgun metagenome libraries resolved 351 distinct genomes from hot-spring (30–45 °C) and mesophilic (17 °C) sediments. Annotation of 39 refined draft genomes revealed metabolism consistent with oligotrophy

    更新日期:2020-11-02
  • Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)
    ISME J. (IF 9.18) Pub Date : 2020-11-02
    Aurélien Lecoeuvre; Bénédicte Ménez; Mathilde Cannat; Valérie Chavagnac; Emmanuelle Gérard

    Lost City (mid-Atlantic ridge) is a unique oceanic hydrothermal field where carbonate-brucite chimneys are colonized by a single phylotype of archaeal Methanosarcinales, as well as sulfur- and methane-metabolizing bacteria. So far, only one submarine analog of Lost City has been characterized, the Prony Bay hydrothermal field (New Caledonia), which nonetheless shows more microbiological similarities

    更新日期:2020-11-02
  • Correction: NanoSIMS single cell analyses reveal the contrasting nitrogen sources for small phytoplankton
    ISME J. (IF 9.18) Pub Date : 2020-10-23
    Hugo Berthelot; Solange Duhamel; Stéphane L’Helguen; Jean-Francois Maguer; Seaver Wang; Ivona Cetinić; Nicolas Cassar

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-10-28
  • Host specificity of microbiome assembly and its fitness effects in phytoplankton
    ISME J. (IF 9.18) Pub Date : 2020-10-23
    Sara L. Jackrel; Jinny W. Yang; Kathryn C. Schmidt; Vincent J. Denef

    Insights into symbiosis between eukaryotic hosts and their microbiomes have shifted paradigms on what determines host fitness, ecology, and behavior. Questions remain regarding the roles of host versus environment in shaping microbiomes, and how microbiome composition affects host fitness. Using a model system in ecology, phytoplankton, we tested whether microbiomes are host-specific, confer fitness

    更新日期:2020-10-28
  • Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy
    ISME J. (IF 9.18) Pub Date : 2020-10-23
    Frank Xavier Ferrer-González; Brittany Widner; Nicole R. Holderman; John Glushka; Arthur S. Edison; Elizabeth B. Kujawinski; Mary Ann Moran

    The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs

    更新日期:2020-10-28
  • The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae
    ISME J. (IF 9.18) Pub Date : 2020-10-22
    Jake N. Barber; Aysha L. Sezmis; Laura C. Woods; Trenton D. Anderson; Jasmyn M. Voss; Michael J. McDonald

    Microbial communities are comprised of many species that coexist on small spatial scales. This is difficult to explain because many interspecies interactions are competitive, and ecological theory predicts that one species will drive the extinction of another species that competes for the same resource. Conversely, evolutionary theory proposes that natural selection can lead to coexistence by driving

    更新日期:2020-10-28
  • Mucin-derived O -glycans supplemented to diet mitigate diverse microbiota perturbations
    ISME J. (IF 9.18) Pub Date : 2020-10-21
    K. M. Pruss; A. Marcobal; A. M. Southwick; D. Dahan; S. A. Smits; J. A. Ferreyra; S. K. Higginbottom; E. D. Sonnenburg; P. C. Kashyap; B. Choudhury; L. Bode; J. L. Sonnenburg

    Microbiota-accessible carbohydrates (MACs) are powerful modulators of microbiota composition and function. These substrates are often derived from diet, such as complex polysaccharides from plants or human milk oligosaccharides (HMOs) during breastfeeding. Host-derived mucus glycans on gut-secreted mucin proteins serve as a continuous endogenous source of MACs for resident microbes; here we investigate

    更新日期:2020-10-28
  • Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13 C and 2 H metabolic network mapping
    ISME J. (IF 9.18) Pub Date : 2020-10-20
    Christopher E. Lawson; Guylaine H. L. Nuijten; Rob M. de Graaf; Tyler B. Jacobson; Martin Pabst; David. M. Stevenson; Mike S. M. Jetten; Daniel R. Noguera; Katherine D. McMahon; Daniel Amador-Noguez; Sebastian Lücker

    Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions

    更新日期:2020-10-20
  • Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon
    ISME J. (IF 9.18) Pub Date : 2020-10-20
    Marie E. Kroeger; Laura K. Meredith; Kyle M. Meyer; Kevin D. Webster; Plinio Barbosa de Camargo; Leandro Fonseca de Souza; Siu Mui Tsai; Joost van Haren; Scott Saleska; Brendan J. M. Bohannan; Jorge L. Mazza Rodrigues; Erika Berenguer; Jos Barlow; Klaus Nüsslein

    The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact

    更新日期:2020-10-20
  • Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection
    ISME J. (IF 9.18) Pub Date : 2020-10-19
    Franziska A. Stressmann; Joaquín Bernal-Bayard; David Perez-Pascual; Bianca Audrain; Olaya Rendueles; Valérie Briolat; Sebastian Bruchmann; Stevenn Volant; Amine Ghozlane; Susanne Häussler; Eric Duchaud; Jean-Pierre Levraud; Jean-Marc Ghigo

    The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a

    更新日期:2020-10-19
  • Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans
    ISME J. (IF 9.18) Pub Date : 2020-10-19
    Jaqueline Hess; Sudhagar V. Balasundaram; Renee I. Bakkemo; Elodie Drula; Bernard Henrissat; Nils Högberg; Daniel Eastwood; Inger Skrede

    Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution

    更新日期:2020-10-19
  • Microbial competition reduces metabolic interaction distances to the low µm-range
    ISME J. (IF 9.18) Pub Date : 2020-10-19
    Rinke J. van Tatenhove-Pel; Tomaž Rijavec; Aleš Lapanje; Iris van Swam; Emile Zwering; Jhonatan A. Hernandez-Valdes; Oscar P. Kuipers; Cristian Picioreanu; Bas Teusink; Herwig Bachmann

    Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal

    更新日期:2020-10-19
  • Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system
    ISME J. (IF 9.18) Pub Date : 2020-10-16
    Leandro D. Guerrero; María V. Pérez; Esteban Orellana; Mariana Piuri; Cecilia Quiroga; Leonardo Erijman

    Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage–host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage–host interactions have been seldom recorded in complex natural environments

    更新日期:2020-10-17
  • Space and patchiness affects diversity–function relationships in fungal decay communities
    ISME J. (IF 9.18) Pub Date : 2020-10-16
    Jade O’Leary; Katie L. Journeaux; Kas Houthuijs; Jasper Engel; Ulf Sommer; Mark R. Viant; Daniel C. Eastwood; Carsten Müller; Lynne Boddy

    The space in which organisms live determines health and physicality, shaping the way in which they interact with their peers. Space, therefore, is critically important for species diversity and the function performed by individuals within mixed communities. The biotic and abiotic factors defined by the space that organisms occupy are ecologically significant and the difficulty in quantifying space-defined

    更新日期:2020-10-17
  • Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline
    ISME J. (IF 9.18) Pub Date : 2020-10-16
    K. Scarlett; S. Denman; D. R. Clark; J. Forster; E. Vanguelova; N. Brown; C. Whitby

    Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree

    更新日期:2020-10-17
  • Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting
    ISME J. (IF 9.18) Pub Date : 2020-10-16
    Anna J. Mueller; Man-Young Jung; Cameron R. Strachan; Craig W. Herbold; Rasmus H. Kirkegaard; Michael Wagner; Holger Daims

    Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting,

    更新日期:2020-10-17
  • Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy
    ISME J. (IF 9.18) Pub Date : 2020-10-15
    Kyle S. Metcalfe; Ranjani Murali; Sean W. Mullin; Stephanie A. Connon; Victoria J. Orphan

    Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia

    更新日期:2020-10-16
  • Life-history strategies of soil microbial communities in an arid ecosystem
    ISME J. (IF 9.18) Pub Date : 2020-10-13
    Yongjian Chen; Julia W. Neilson; Priyanka Kushwaha; Raina M. Maier; Albert Barberán

    The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial

    更新日期:2020-10-13
  • Extracellular heme recycling and sharing across species by novel mycomembrane vesicles of a Gram-positive bacterium
    ISME J. (IF 9.18) Pub Date : 2020-10-09
    Meng Wang; Yong Nie; Xiao-Lei Wu

    Microbes spontaneously release membrane vesicles (MVs), which play roles in nutrient acquisition and microbial interactions. Iron is indispensable for microbes, but is a difficult nutrient to acquire. However, whether MVs are also responsible for efficient iron uptake and therefore involved in microbial interaction remains to be elucidated. Here, we used a Gram-positive strain, Dietzia sp. DQ12-45-1b

    更新日期:2020-10-11
  • Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean
    ISME J. (IF 9.18) Pub Date : 2020-10-08
    Kevin W. Becker; Matthew J. Harke; Daniel R. Mende; Daniel Muratore; Joshua S. Weitz; Edward F. DeLong; Sonya T. Dyhrman; Benjamin A. S. Van Mooy

    Sunlight is the most important environmental control on diel fluctuations in phytoplankton activity, and understanding diel microbial processes is essential to the study of oceanic biogeochemical cycles. Yet, little is known about the in situ temporal dynamics of phytoplankton metabolic activities and their coordination across different populations. We investigated diel orchestration of phytoplankton

    更新日期:2020-10-08
  • Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms
    ISME J. (IF 9.18) Pub Date : 2020-10-07
    Charles Bernard; Yanyan Li; Philippe Lopez; Eric Bapteste

    The evolutionary stability of temperate bacteriophages at low abundance of susceptible bacterial hosts lies in the trade-off between the maximization of phage replication, performed by the host-destructive lytic cycle, and the protection of the phage-host collective, enacted by lysogeny. Upon Bacillus infection, Bacillus phages phi3T rely on the “arbitrium” quorum sensing (QS) system to communicate

    更新日期:2020-10-07
  • Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment
    ISME J. (IF 9.18) Pub Date : 2020-10-07
    Kunkun Fan; Manuel Delgado-Baquerizo; Xisheng Guo; Daozhong Wang; Yong-guan Zhu; Haiyan Chu

    Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing

    更新日期:2020-10-07
  • Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease
    ISME J. (IF 9.18) Pub Date : 2020-10-07
    Sang-Moo Lee; Hyun Gi Kong; Geun Cheol Song; Choong-Min Ryu

    Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria

    更新日期:2020-10-07
  • Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
    ISME J. (IF 9.18) Pub Date : 2020-10-07
    Gust Bilcke; Koen Van den Berge; Sam De Decker; Eli Bonneure; Nicole Poulsen; Petra Bulankova; Cristina Maria Osuna-Cruz; Jack Dickenson; Koen Sabbe; Georg Pohnert; Klaas Vandepoele; Sven Mangelinckx; Lieven Clement; Lieven De Veylder; Wim Vyverman

    Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in natural circumstances and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatom Seminavis robusta. We observe

    更新日期:2020-10-07
  • Acidobacteria are active and abundant members of diverse atmospheric H 2 -oxidizing communities detected in temperate soils
    ISME J. (IF 9.18) Pub Date : 2020-10-06
    Andrew T. Giguere; Stephanie A. Eichorst; Dimitri V. Meier; Craig W. Herbold; Andreas Richter; Chris Greening; Dagmar Woebken

    Significant rates of atmospheric hydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse

    更新日期:2020-10-07
  • Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora
    ISME J. (IF 9.18) Pub Date : 2020-10-06
    Zhouqi Cui; Regan B. Huntley; Quan Zeng; Blaire Steven

    Plant microbiomes have important roles in plant health and productivity. However, despite flowers being directly linked to reproductive outcomes, little is known about the microbiomes of flowers and their potential interaction with pathogen infection. Here, we investigated the temporal spatial dynamics of the apple stigma microbiome when challenged with a phytopathogen Erwinia amylovora, the causal

    更新日期:2020-10-07
  • Rapid evolution destabilizes species interactions in a fluctuating environment
    ISME J. (IF 9.18) Pub Date : 2020-10-06
    Alejandra Rodríguez-Verdugo; Martin Ackermann

    Positive species interactions underlie the functioning of ecosystems. Given their importance, it is crucial to understand the stability of positive interactions over evolutionary timescales, in both constant and fluctuating environments; e.g., environments interrupted with periods of competition. We addressed this question using a two-species microbial system in which we modulated interactions according

    更新日期:2020-10-07
  • Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts
    ISME J. (IF 9.18) Pub Date : 2020-10-03
    Jessica A. Taylor; Giorgia Palladino; Bernd Wemheuer; Georg Steinert; Detmer Sipkema; Timothy J. Williams; Torsten Thomas

    The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth

    更新日期:2020-10-04
  • Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
    ISME J. (IF 9.18) Pub Date : 2020-10-03
    Sean Meaden; Loris Capria; Ellinor Alseth; Sylvain Gandon; Ambarish Biswas; Luca Lenzi; Stineke van Houte; Edze R. Westra

    CRISPR-Cas immune systems are widespread in bacteria and archaea, but not ubiquitous. Previous work has demonstrated that CRISPR immunity is associated with an infection-induced fitness cost, which may help explain the patchy distribution observed. However, the mechanistic basis of this cost has remained unclear. Using Pseudomonas aeruginosa PA14 and its phage DMS3vir as a model, we perform a 30-day

    更新日期:2020-10-04
  • Wildland fire as an atmospheric source of viable microbial aerosols and biological ice nucleating particles
    ISME J. (IF 9.18) Pub Date : 2020-10-02
    Rachel A. Moore; Chelsey Bomar; Leda N. Kobziar; Brent C. Christner

    The environmental sources of microbial aerosols and processes by which they are emitted into the atmosphere are not well characterized. In this study we analyzed microbial cells and biological ice nucleating particles (INPs) in smoke emitted from eight prescribed wildland fires in North Florida. When compared to air sampled prior to ignition, samples of the air–smoke mixtures contained fivefold higher

    更新日期:2020-10-02
  • Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes
    ISME J. (IF 9.18) Pub Date : 2020-10-01
    Stefan Geisen; Shunran Hu; Thomas Edison E. dela Cruz; G. F. (Ciska) Veen

    Soil bacteria and fungi are key drivers of carbon released from soils to the atmosphere through decomposition of plant-derived organic carbon sources. This process has important consequences for the global climate. While global change factors, such as increased temperature, are known to affect bacterial- and fungal-mediated decomposition rates, the role of trophic interactions in affecting decomposition

    更新日期:2020-10-02
  • Direct interactions with commensal streptococci modify intercellular communication behaviors of Streptococcus mutans
    ISME J. (IF 9.18) Pub Date : 2020-09-30
    Justin R. Kaspar; Kyulim Lee; Brook Richard; Alejandro R. Walker; Robert A. Burne

    The formation of dental caries is a complex process that ultimately leads to damage of the tooth enamel from acids produced by microbes in attached biofilms. The bacterial interactions occurring within these biofilms between cariogenic bacteria, such as the mutans streptococci, and health-associated commensal streptococci, are thought to be critical determinants of health and disease. To better understand

    更新日期:2020-09-30
  • Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage
    ISME J. (IF 9.18) Pub Date : 2020-09-30
    Xiao Chu; Siyao Li; Sishuo Wang; Danli Luo; Haiwei Luo

    Ecologically relevant genes generally show patchy distributions among related bacterial genomes. This is commonly attributed to lateral gene transfer, whereas the opposite mechanism—gene loss—has rarely been explored. Pseudogenization is a major mechanism underlying gene loss, and pseudogenes are best characterized by comparing closely related genomes because of their short life spans. To explore the

    更新日期:2020-09-30
  • Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies
    ISME J. (IF 9.18) Pub Date : 2020-09-28
    Anouk van’t Padje; Loreto Oyarte Galvez; Malin Klein; Mark A. Hink; Marten Postma; Thomas Shimizu; E. Toby Kiers

    Arbuscular mycorrhizal fungi function as conduits for underground nutrient transport. While the fungal partner is dependent on the plant host for its carbon (C) needs, the amount of nutrients that the fungus allocates to hosts can vary with context. Because fungal allocation patterns to hosts can change over time, they have historically been difficult to quantify accurately. We developed a technique

    更新日期:2020-09-28
  • Achieving similar root microbiota composition in neighbouring plants through airborne signalling.
    ISME J. (IF 9.18) Pub Date : 2020-09-24
    Hyun Gi Kong,Geun Cheol Song,Hee-Jung Sim,Choong-Min Ryu

    The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is

    更新日期:2020-09-24
  • A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus.
    ISME J. (IF 9.18) Pub Date : 2020-09-23
    Corey Nelson,Ana Giraldo-Silva,Ferran Garcia-Pichel

    Microcoleus vaginatus plays a prominent role as both primary producer and pioneer in biocrust communities from dryland soils. And yet, it cannot fix dinitrogen, essential in often nitrogen-limited drylands. But a diazotroph-rich “cyanosphere” has been described in M. vaginatus, hinting that there exists a C for N exchange between the photoautotroph and heterotrophic diazotrophs. We provide evidence

    更新日期:2020-09-24
  • Independent iron and light limitation in a low-light-adapted Prochlorococcus from the deep chlorophyll maximum.
    ISME J. (IF 9.18) Pub Date : 2020-09-23
    Nicholas J Hawco,Feixue Fu,Nina Yang,David A Hutchins,Seth G John

    Throughout the open ocean, a minimum in dissolved iron concentration (dFe) overlaps with the deep chlorophyll maximum (DCM), which marks the lower limit of the euphotic zone. Maximizing light capture in these dim waters is expected to require upregulation of Fe-bearing photosystems, further depleting dFe and possibly leading to co-limitation by both iron and light. However, this effect has not been

    更新日期:2020-09-23
  • Air pollution could drive global dissemination of antibiotic resistance genes.
    ISME J. (IF 9.18) Pub Date : 2020-09-22
    Guibing Zhu,Xiaomin Wang,Ting Yang,Jianqiang Su,Yu Qin,Shanyun Wang,Michael Gillings,Cheng Wang,Feng Ju,Bangrui Lan,Chunlei Liu,Hu Li,Xi-En Long,Xuming Wang,Mike S M Jetten,Zifa Wang,Yong-Guan Zhu

    Antibiotic-resistant pathogens pose a significant threat to human health. Several dispersal mechanisms have been described, but transport of both microbes and antibiotic resistance genes (ARGs) via atmospheric particles has received little attention as a pathway for global dissemination. These atmospheric particles can return to the Earth’s surface via rain or snowfall, and thus promote long-distance

    更新日期:2020-09-23
  • Two-way microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging.
    ISME J. (IF 9.18) Pub Date : 2020-09-22
    Shifra Steinberg,Maor Grinberg,Michael Beitelman,Julianna Peixoto,Tomer Orevi,Nadav Kashtan

    The phyllosphere – the aerial parts of plants – is an important microbial habitat that is home to diverse microbial communities. The spatial organization of bacterial cells on leaf surfaces is non-random, and correlates with leaf microscopic features. Yet, the role of microscale interactions between bacterial cells therein is not well understood. Here, we ask how interactions between immigrant bacteria

    更新日期:2020-09-22
  • A network approach to elucidate and prioritize microbial dark matter in microbial communities.
    ISME J. (IF 9.18) Pub Date : 2020-09-22
    Tatyana Zamkovaya,Jamie S Foster,Valérie de Crécy-Lagard,Ana Conesa

    Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter,” represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment

    更新日期:2020-09-22
  • Environmental pH is a key modulator of Staphylococcus aureus biofilm development under predation by the virulent phage phiIPLA-RODI.
    ISME J. (IF 9.18) Pub Date : 2020-09-22
    Lucía Fernández,Diana Gutiérrez,Pilar García,Ana Rodríguez

    Previous work had shown that, in some Staphylococcus aureus strains, low concentrations of the virulent phage vB_SauM_phiIPLA-RODI (phiIPLA-RODI) promoted the formation of DNA-rich biofilms, whose cells exhibited significant transcriptional differences compared to an uninfected control. This study aimed to dissect the sequence of events leading to these changes. Analysis of phage propagation throughout

    更新日期:2020-09-22
  • Biofilm matrix disrupts nematode motility and predatory behavior.
    ISME J. (IF 9.18) Pub Date : 2020-09-21
    Shepherd Yuen Chan,Sylvia Yang Liu,Zijing Seng,Song Lin Chua

    In nature, bacteria form biofilms by producing exopolymeric matrix that encases its entire community. While it is widely known that biofilm matrix can prevent bacterivore predation and contain virulence factors for killing predators, it is unclear if they can alter predator motility. Here, we report a novel “quagmire” phenotype, where Pseudomonas aeruginosa biofilms could retard the motility of bacterivorous

    更新日期:2020-09-21
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