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
  • Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study
    ISME J. (IF 9.18) Pub Date : 2020-09-19
    Andrew R. St. James; Joseph B. Yavitt; Stephen H. Zinder; Ruth E. Richardson

    Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis

  • Quorum sensing controls persistence, resuscitation, and virulence of Legionella subpopulations in biofilms
    ISME J. (IF 9.18) Pub Date : 2020-09-19
    Nicolas Personnic; Bianca Striednig; Hubert Hilbi

    The water-borne bacterium Legionella pneumophila is the causative agent of Legionnaires’ disease. In the environment, the opportunistic pathogen colonizes different niches, including free-living protozoa and biofilms. The physiological state(s) of sessile Legionella in biofilms and their functional consequences are not well understood. Using single-cell techniques and fluorescent growth rate probes

  • Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation
    ISME J. (IF 9.18) Pub Date : 2020-09-17
    Meng-Yun Chen; Wen-Kai Teng; Liang Zhao; Chun-Xiang Hu; Yang-Kai Zhou; Bo-Ping Han; Li-Rong Song; Wen-Sheng Shu

    Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater,

  • Benchmarking microbial growth rate predictions from metagenomes
    ISME J. (IF 9.18) Pub Date : 2020-09-16
    Andrew M. Long; Shengwei Hou; J. Cesar Ignacio-Espinoza; Jed A. Fuhrman

    Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and “peak-to-trough ratio” (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to

  • Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris
    ISME J. (IF 9.18) Pub Date : 2020-09-15
    Bo Wu; Feifei Liu; Aifen Zhou; Juan Li; Longfei Shu; Megan L. Kempher; Xueqin Yang; Daliang Ning; Feiyan Pan; Grant M. Zane; Judy D. Wall; Joy D. Van Nostrand; Philippe Juneau; Shouwen Chen; Qingyun Yan; Jizhong Zhou; Zhili He

    Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough

  • Temperature transcends partner specificity in the symbiosis establishment of a cnidarian
    ISME J. (IF 9.18) Pub Date : 2020-09-15
    Marcela Herrera; Shannon G. Klein; Sara Campana; Jit Ern Chen; Arun Prasanna; Carlos M. Duarte; Manuel Aranda

    Coral reef research has predominantly focused on the effect of temperature on the breakdown of coral-dinoflagellate symbioses. However, less is known about how increasing temperature affects the establishment of new coral-dinoflagellate associations. Inter-partner specificity and environment-dependent colonization are two constraints proposed to limit the acquisition of more heat tolerant symbionts

  • Frequency of mispackaging of Prochlorococcus DNA by cyanophage
    ISME J. (IF 9.18) Pub Date : 2020-09-14
    Raphaël Laurenceau; Nicolas Raho; Mathieu Forget; Aldo A. Arellano; Sallie W. Chisholm

    Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages—a podovirus, a siphovirus, and a myovirus—to mispackage host DNA in their capsids while

  • Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide
    ISME J. (IF 9.18) Pub Date : 2020-09-14
    Belinda C. Martin; Jen A. Middleton; Matthew W. Fraser; Ian P. G. Marshall; Vincent V. Scholz; Bertram Hausl; Hannes Schmidt

    Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems

  • Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids
    ISME J. (IF 9.18) Pub Date : 2020-09-14
    Laura Villanueva; F. A. Bastiaan von Meijenfeldt; Alexander B. Westbye; Subhash Yadav; Ellen C. Hopmans; Bas E. Dutilh; Jaap S. Sinninghe Damsté

    Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/Eukarya produce membranes consisting of fatty acids ester-bound to glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the ‘lipid divide’) is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed

  • Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
    ISME J. (IF 9.18) Pub Date : 2020-09-14
    Live H. Hagen; Charles G. Brooke; Claire A. Shaw; Angela D. Norbeck; Hailan Piao; Magnus Ø. Arntzen; Heather M. Olson; Alex Copeland; Nancy Isern; Anil Shukla; Simon Roux; Vincent Lombard; Bernard Henrissat; Michelle A. O’Malley; Igor V. Grigoriev; Susannah G. Tringe; Roderick I. Mackie; Ljiljana Pasa-Tolic; Phillip B. Pope; Matthias Hess

    The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically

  • Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate
    ISME J. (IF 9.18) Pub Date : 2020-09-12
    Ramon Massana; Aurelie Labarre; David López-Escardó; Aleix Obiol; François Bucchini; Thomas Hackl; Matthias G. Fischer; Klaas Vandepoele; Denis V. Tikhonenkov; Filip Husnik; Patrick J. Keeling

    Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed

  • Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A
    ISME J. (IF 9.18) Pub Date : 2020-09-11
    Francisco M. Cornejo-Castillo; Jonathan P. Zehr

    Non-cyanobacterial diazotrophs (NCDs) have recently emerged as potentially important contributors to marine nitrogen fixation. One of the most widely distributed NCDs is Gamma-A, yet information about its autecology is still scarce and solely relies on the PCR-based detection of its nitrogenase (nifH) gene in seawater, since previous metagenomic surveys targeting free-living planktonic size fractions

  • A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances
    ISME J. (IF 9.18) Pub Date : 2020-09-11
    Noor Mruwat; Michael C. G. Carlson; Svetlana Goldin; François Ribalet; Shay Kirzner; Yotam Hulata; Stephen J. Beckett; Dror Shitrit; Joshua S. Weitz; E. Virginia Armbrust; Debbie Lindell

    Long-term stability of picocyanobacteria in the open oceans is maintained by a balance between synchronous division and death on daily timescales. Viruses are considered a major source of microbial mortality, however, current methods to measure infection have significant methodological limitations. Here we describe a method that pairs flow-cytometric sorting with a PCR-based polony technique to simultaneously

  • Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity
    ISME J. (IF 9.18) Pub Date : 2020-09-07
    Elena V. Kozlova; Shivanand Hegde; Christopher M. Roundy; George Golovko; Miguel A. Saldaña; Charles E. Hart; Enyia R. Anderson; Emily A. Hornett; Kamil Khanipov; Vsevolod L. Popov; Maria Pimenova; Yiyang Zhou; Yuriy Fovanov; Scott C. Weaver; Andrew L. Routh; Eva Heinz; Grant L. Hughes

    How microbe–microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found that, Serratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonized Aedes aegypti yet was abundant in Culex quinquefasciatus reared under identical conditions. To investigate the incompatibility between Serratia and Ae. aegypti, we characterized

  • Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment.
    ISME J. (IF 9.18) Pub Date : 2020-09-04
    Nicholas J Reichart,Zackary J Jay,Viola Krukenberg,Albert E Parker,Rachel L Spietz,Roland Hatzenpichler

    Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing

  • The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.
    ISME J. (IF 9.18) Pub Date : 2020-09-04
    Chun-Hui Gao,Hui Cao,Peng Cai,Søren J Sørensen

    Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated

  • Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity.
    ISME J. (IF 9.18) Pub Date : 2020-09-04
    Zhao Wang,Despina Tsementzi,Tiffany C Williams,Doris L Juarez,Sara K Blinebry,Nathan S Garcia,Brooke K Sienkiewicz,Konstantinos T Konstantinidis,Zackary I Johnson,Dana E Hunt

    Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations with larger diel, episodic, and annual variability in temperature and pH should be less sensitive to shifts in these climate-change factors. To test

  • To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators.
    ISME J. (IF 9.18) Pub Date : 2020-09-03
    Rajesh Sathyamoorthy,Yuval Kushmaro,Or Rotem,Ofra Matan,Daniel E Kadouri,Amit Huppert,Edouard Jurkevitch

    The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives

  • Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community.
    ISME J. (IF 9.18) Pub Date : 2020-09-03
    Daniel Padfield,Alex Vujakovic,Steve Paterson,Rob Griffiths,Angus Buckling,Elze Hesse

    Rapid within-species evolution can alter community structure, yet the mechanisms underpinning this effect remain unknown. Populations that rapidly evolve large amounts of phenotypic diversity are likely to interact with more species and have the largest impact on community structure. However, the evolution of phenotypic diversity is, in turn, influenced by the presence of other species. Here, we investigate

  • A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas.
    ISME J. (IF 9.18) Pub Date : 2020-09-02
    Zilia Y Muñoz-Ramirez,Ben Pascoe,Alfonso Mendez-Tenorio,Evangelos Mourkas,Santiago Sandoval-Motta,Guillermo Perez-Perez,Douglas R Morgan,Ricardo Leonel Dominguez,Diana Ortiz-Princz,Maria Eugenia Cavazza,Gifone Rocha,Dulcienne M M Queiroz,Mariana Catalano,Gerardo Zerbeto de la Palma,Cinthia G Goldman,Alejandro Venegas,Teresa Alarcon,Monica Oleastro,Filipa F Vale,Karen J Goodman,Roberto C Torres,Elvire

    Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry has led to the development of genetically distinct H. pylori subpopulations, associated with different human populations, and more recent admixture among H. pylori subpopulations can provide information about human migrations

  • Cytometric fingerprints of gut microbiota predict Crohn's disease state.
    ISME J. (IF 9.18) Pub Date : 2020-09-02
    Peter Rubbens,Ruben Props,Frederiek-Maarten Kerckhof,Nico Boon,Willem Waegeman

    Variations in the gut microbiome have been associated with changes in health state such as Crohn’s disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected

  • Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.
    ISME J. (IF 9.18) Pub Date : 2020-09-02
    Maria Mooshammer,Katharina Kitzinger,Arno Schintlmeister,Soeren Ahmerkamp,Jeppe Lund Nielsen,Per Halkjær Nielsen,Michael Wagner

    Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms

  • Microbial carrying capacity and carbon biomass of plastic marine debris.
    ISME J. (IF 9.18) Pub Date : 2020-09-02
    Shiye Zhao,Erik R Zettler,Linda A Amaral-Zettler,Tracy J Mincer

    Trillions of plastic debris fragments are floating at sea, presenting a substantial surface area for microbial colonization. Numerous cultivation-independent surveys have characterized plastic-associated microbial biofilms, however, quantitative studies addressing microbial carbon biomass are lacking. Our confocal laser scanning microscopy data show that early biofilm development on polyethylene, polypropylene

  • Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens.
    ISME J. (IF 9.18) Pub Date : 2020-09-02
    Pilar Vesga,Pascale Flury,Jordan Vacheron,Christoph Keel,Daniel Croll,Monika Maurhofer

    Pseudomonas protegens shows a high degree of lifestyle plasticity since it can establish both plant-beneficial and insect-pathogenic interactions. While P. protegens protects plants against soilborne pathogens, it can also invade insects when orally ingested leading to the death of susceptible pest insects. The mechanism whereby pseudomonads effectively switch between lifestyles, plant-beneficial or

  • The cell organization underlying structural colour is involved in Flavobacterium IR1 predation.
    ISME J. (IF 9.18) Pub Date : 2020-09-01
    Raditijo Hamidjaja,Jérémie Capoulade,Laura Catón,Colin J Ingham

    Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and

  • Direct quantification of ecological drift at the population level in synthetic bacterial communities.
    ISME J. (IF 9.18) Pub Date : 2020-08-27
    Stilianos Fodelianakis,Adriana Valenzuela-Cuevas,Alan Barozzi,Daniele Daffonchio

    In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and

  • Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria.
    ISME J. (IF 9.18) Pub Date : 2020-08-24
    Caroline L Monteil,Karim Benzerara,Nicolas Menguy,Cécile C Bidaud,Emmanuel Michot-Achdjian,Romain Bolzoni,François P Mathon,Margot Coutaud,Béatrice Alonso,Camille Garau,Didier Jézéquel,Eric Viollier,Nicolas Ginet,Magali Floriani,Sufal Swaraj,Martin Sachse,Vincent Busigny,Elodie Duprat,François Guyot,Christopher T Lefevre

    Bacteria synthesize a wide range of intracellular submicrometer-sized inorganic precipitates of diverse chemical compositions and structures, called biominerals. Their occurrences, functions and ultrastructures are not yet fully described despite great advances in our knowledge of microbial diversity. Here, we report bacteria inhabiting the sediments and water column of the permanently stratified ferruginous

  • The saccharibacterium TM7x elicits differential responses across its host range.
    ISME J. (IF 9.18) Pub Date : 2020-08-24
    Daniel R Utter,Xuesong He,Colleen M Cavanaugh,Jeffrey S McLean,Batbileg Bor

    Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the

  • Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians.
    ISME J. (IF 9.18) Pub Date : 2020-08-21
    Mariko Kishimoto,Andrew H Baird,Shinichiro Maruyama,Jun Minagawa,Shunichi Takahashi

    Increases in seawater temperature can cause coral bleaching through loss of symbiotic algae (dinoflagellates of the family Symbiodiniaceae). Corals can recover from bleaching by recruiting algae into host cells from the residual symbiont population or from the external environment. However, the high coral mortality that often follows mass-bleaching events suggests that recovery is often limited in

  • Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes.
    ISME J. (IF 9.18) Pub Date : 2020-08-20
    Zhichao Zhou,Yang Liu,Jie Pan,Brandi R Cron,Brandy M Toner,Karthik Anantharaman,John A Breier,Gregory J Dick,Meng Li

    Deep-sea hydrothermal plumes are considered natural laboratories for understanding ecological and biogeochemical interactions. Previous studies focused on interactions between microorganisms and inorganic, reduced hydrothermal inputs including sulfur, hydrogen, iron, and manganese. However, little is known about transformations of organic compounds, especially methylated, sulfur-containing compounds

  • Presence of toxin-antitoxin systems in picocyanobacteria and their ecological implications.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Daniel Fucich,Feng Chen

    Picocyanobacteria (mainly Synechococcus and Prochlorococcus) contribute significantly to ocean’s primary production. Toxin-Antitoxin (TA) systems present in bacteria and archaea are known to regulate cell growth in response to environmental stresses. However, little is known about the presence of TA systems in picocyanobacteria. This study investigated complete genomes of Synechococcus and Prochlorococcus

  • Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Xiaojun Wang,Yao Zhang,Minglei Ren,Tingying Xia,Xiao Chu,Chang Liu,Xingqin Lin,Yongjie Huang,Zhuoyu Chen,Aixin Yan,Haiwei Luo

    A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria–phage and bacteria–phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the

  • Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Laura Camus,Paul Briaud,Sylvère Bastien,Sylvie Elsen,Anne Doléans-Jordheim,François Vandenesch,Karen Moreau

    In the context of infection, Pseudomonas aeruginosa and Staphylococcus aureus are frequently co-isolated, particularly in cystic fibrosis (CF) patients. Within lungs, the two pathogens exhibit a range of competitive and coexisting interactions. In the present study, we explored the impact of S. aureus on the physiology of P. aeruginosa in the context of coexistence. Transcriptomic analyses showed that

  • Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Rhona K Stuart,Eric R A Pederson,Philip D Weyman,Peter K Weber,Ulla Rassmussen,Christopher L Dupont

    In nitrogen-limited boreal forests, associations between feathermoss and diazotrophic cyanobacteria control nitrogen inputs and thus carbon cycling, but little is known about the molecular regulators required for initiation and maintenance of these associations. Specifically, a benefit to the cyanobacteria is not known, challenging whether the association is a nutritional mutualism. Targeted mutagenesis

  • An invasive beetle-fungus complex is maintained by fungal nutritional-compensation mediated by bacterial volatiles.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Fanghua Liu,Jacob D Wickham,Qingjie Cao,Min Lu,Jianghua Sun

    Mutualisms between symbiotic microbes and animals have been well documented, and nutritional relationships provide the foundation for maintaining beneficial associations. The well-studied mutualism between bark beetles and their fungi has become a classic model system in the study of symbioses. Despite the nutritional competition between bark beetles and beneficial fungi in the same niche due to poor

  • A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases.
    ISME J. (IF 9.18) Pub Date : 2020-08-19
    Binnian Tian,Jiatao Xie,Yanping Fu,Jiasen Cheng,Bo Li,Tao Chen,Ying Zhao,Zhixiao Gao,Puyun Yang,Martin J Barbetti,Brett M Tyler,Daohong Jiang

    Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to help safeguard such resources for increasing human populations on a global scale. Here, we find that Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, rice, barley, maize, and oat, providing protection

  • Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline.
    ISME J. (IF 9.18) Pub Date : 2020-08-14
    Paraskevi Mara,Dean Vik,Maria G Pachiadaki,Elizabeth A Suter,Bonnie Poulos,Gordon T Taylor,Matthew B Sullivan,Virginia P Edgcomb

    Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key

  • Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community.
    ISME J. (IF 9.18) Pub Date : 2020-08-12
    Ryan K Fritts,Jordan T Bird,Megan G Behringer,Anna Lipzen,Joel Martin,Michael Lynch,James B McKinlay

    Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding

  • Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought.
    ISME J. (IF 9.18) Pub Date : 2020-08-07
    Joana Séneca,Petra Pjevac,Alberto Canarini,Craig W Herbold,Christos Zioutis,Marlies Dietrich,Eva Simon,Judith Prommer,Michael Bahn,Erich M Pötsch,Michael Wagner,Wolfgang Wanek,Andreas Richter

    Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted

  • Unique inducible filamentous motility identified in pathogenic Bacillus cereus group species.
    ISME J. (IF 9.18) Pub Date : 2020-08-07
    Martha M Liu,Shannon Coleman,Lauren Wilkinson,Maren L Smith,Thomas Hoang,Naomi Niyah,Manjari Mukherjee,Steven Huynh,Craig T Parker,Jasna Kovac,Robert E W Hancock,Erin C Gaynor

    Active migration across semi-solid surfaces is important for bacterial success by facilitating colonization of unoccupied niches and is often associated with altered virulence and antibiotic resistance profiles. We isolated an atmospheric contaminant, subsequently identified as a new strain of Bacillus mobilis, which showed a unique, robust, rapid, and inducible filamentous surface motility. This

  • A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities.
    ISME J. (IF 9.18) Pub Date : 2020-08-07
    S A Kraemer,N Barbosa da Costa,B J Shapiro,M Fradette,Y Huot,D A Walsh

    Lakes play a pivotal role in ecological and biogeochemical processes and have been described as “sentinels” of environmental change. Assessing “lake health” across large geographic scales is critical to predict the stability of their ecosystem services and their vulnerability to anthropogenic disturbances. The LakePulse research network is tasked with the assessment of lake health across gradients

  • Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat.
    ISME J. (IF 9.18) Pub Date : 2020-08-07
    Judith M Klatt,Gonzalo V Gomez-Saez,Steffi Meyer,Petra Pop Ristova,Pelin Yilmaz,Michael S Granitsiotis,Jennifer L Macalady,Gaute Lavik,Lubos Polerecky,Solveig I Bühring

    Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with

  • Fungal communities decline with urbanization-more in air than in soil.
    ISME J. (IF 9.18) Pub Date : 2020-08-05
    Nerea Abrego,Brittni Crosier,Panu Somervuo,Natalia Ivanova,Arusyak Abrahamyan,Amir Abdi,Karoliina Hämäläinen,Kaisa Junninen,Minna Maunula,Jenna Purhonen,Otso Ovaskainen

    Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially due to the methodological difficulties in comprehensively

  • Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria.
    ISME J. (IF 9.18) Pub Date : 2020-08-04
    Mario K C Krespach,María García-Altares,Michal Flak,Hanno Schoeler,Kirstin Scherlach,Tina Netzker,Anica Schmalzl,Derek J Mattern,Volker Schroeckh,Anna Komor,Maria Mittag,Christian Hertweck,Axel A Brakhage

    Organismal interactions within microbial consortia and their responses to harmful intruders remain largely understudied. An important step toward the goal of understanding functional ecological interactions and their evolutionary selection is the study of increasingly complex microbial interaction systems. Here, we discovered a tripartite biosystem consisting of the fungus Aspergillus nidulans, the

  • Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.
    ISME J. (IF 9.18) Pub Date : 2020-08-03
    Robert Pieper,Temesgen H Dadi,Laura Pieper,Wilfried Vahjen,André Franke,Knut Reinert,Jürgen Zentek

    Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal

  • Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes.
    ISME J. (IF 9.18) Pub Date : 2020-08-03
    J M Tsuji,N Tran,S L Schiff,J J Venkiteswaran,L A Molot,M Tank,S Hanada,J D Neufeld

    Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron–sulfur microbiology of these systems has been poorly

  • Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation.
    ISME J. (IF 9.18) Pub Date : 2020-07-30
    Jorge A M de Sousa,Amandine Buffet,Matthieu Haudiquet,Eduardo P C Rocha,Olaya Rendueles

    Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the

  • A spore quality-quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis.
    ISME J. (IF 9.18) Pub Date : 2020-07-28
    Alper Mutlu,Charlotte Kaspar,Nils Becker,Ilka B Bischofs

    Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated

  • Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system.
    ISME J. (IF 9.18) Pub Date : 2020-07-27
    Paula Huber,Sebastian Metz,Fernando Unrein,Gisela Mayora,Hugo Sarmento,Melina Devercelli

    How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection

  • Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease.
    ISME J. (IF 9.18) Pub Date : 2020-07-27
    Zhang Wang,Yuqiong Yang,Zhengzheng Yan,Haiyue Liu,Boxuan Chen,Zhenyu Liang,Fengyan Wang,Bruce E Miller,Ruth Tal-Singer,Xinzhu Yi,Jintian Li,Martin R Stampfli,Hongwei Zhou,Christopher E Brightling,James R Brown,Martin Wu,Rongchang Chen,Wensheng Shu

    The interaction between airway microbiome and host in chronic obstructive pulmonary disease (COPD) is poorly understood. Here we used a multi-omic meta-analysis approach to characterize the functional signature of airway microbiome in COPD. We retrieved all public COPD sputum microbiome datasets, totaling 1640 samples from 16S rRNA gene datasets and 26 samples from metagenomic datasets from across

  • Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira.
    ISME J. (IF 9.18) Pub Date : 2020-07-24
    Anne Daebeler,Katharina Kitzinger,Hanna Koch,Craig W Herbold,Michaela Steinfeder,Jasmin Schwarz,Thomas Zechmeister,Søren M Karst,Mads Albertsen,Per H Nielsen,Michael Wagner,Holger Daims

    Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology

  • Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations.
    ISME J. (IF 9.18) Pub Date : 2020-07-24
    Eleonora Chiri,Chris Greening,Rachael Lappan,David W Waite,Thanavit Jirapanjawat,Xiyang Dong,Stefan K Arndt,Philipp A Nauer

    Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic CH4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia

  • Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms.
    ISME J. (IF 9.18) Pub Date : 2020-07-20
    Rebecca E Cooper,Carl-Eric Wegner,Stefan Kügler,Remington X Poulin,Nico Ueberschaar,Jens D Wurlitzer,Daniel Stettin,Thomas Wichard,Georg Pohnert,Kirsten Küsel

    Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or –oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded

  • Intracellular symbionts drive sex ratio in the whitefly by facilitating fertilization and provisioning of B vitamins.
    ISME J. (IF 9.18) Pub Date : 2020-07-20
    Yan-Bin Wang,Fei-Rong Ren,Ya-Lin Yao,Xiang Sun,Linda L Walling,Na-Na Li,Bing Bai,Xi-Yu Bao,Xiao-Rui Xu,Jun-Bo Luan

    Symbionts can regulate animal reproduction in multiple ways, but the underlying physiological and biochemical mechanisms remain largely unknown. The presence of multiple lineages of maternally inherited, intracellular symbionts (the primary and secondary symbionts) in terrestrial arthropods is widespread in nature. However, the biological, metabolic, and evolutionary role of co-resident secondary symbionts

  • The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects.
    ISME J. (IF 9.18) Pub Date : 2020-07-17
    Chop Yan Lee,Juan Manuel Peralta-Sánchez,Manuel Martínez-Bueno,Anders Pape Møller,Miguel Rabelo-Ruiz,Carmen Zamora-Muñoz,Juan José Soler

    Gut microbiota are essential for host health and survival, but we are still far from understanding the processes involved in shaping their composition and evolution. Controlled experimental work under lab conditions as well as human studies pointed at environmental factors (i.e., diet) as the main determinant of the microbiota with little evidence of genetic effects, while comparative interspecific

  • Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt.
    ISME J. (IF 9.18) Pub Date : 2020-07-17
    Jun Yuan,Tao Wen,He Zhang,Mengli Zhao,C Ryan Penton,Linda S Thomashow,Qirong Shen

    Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition

  • Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog.
    ISME J. (IF 9.18) Pub Date : 2020-07-17
    Raphaël Méheust,Cindy J Castelle,Paula B Matheus Carnevali,Ibrahim F Farag,Christine He,Lin-Xing Chen,Yuki Amano,Laura A Hug,Jillian F Banfield

    Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including

  • Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation.
    ISME J. (IF 9.18) Pub Date : 2020-07-14
    Carolina Reyes,Logan H Hodgskiss,Melina Kerou,Thomas Pribasnig,Sophie S Abby,Barbara Bayer,Stephan M Kraemer,Christa Schleper

    Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible

  • Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.
    ISME J. (IF 9.18) Pub Date : 2020-07-13
    Jessica K Jarett,Mária Džunková,Frederik Schulz,Simon Roux,David Paez-Espino,Emiley Eloe-Fadrosh,Sean P Jungbluth,Natalia Ivanova,John R Spear,Stephanie A Carr,Christopher B Trivedi,Frank A Corsetti,Hope A Johnson,Eric Becraft,Nikos Kyrpides,Ramunas Stepanauskas,Tanja Woyke

    Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus

  • Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.
    ISME J. (IF 9.18) Pub Date : 2020-07-10
    Laura A Sauder,Mads Albertsen,Katja Engel,Jasmin Schwarz,Per H Nielsen,Michael Wagner,Josh D Neufeld

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

Contents have been reproduced by permission of the publishers.
ACS ES&T Engineering
ACS ES&T Water