Microbial ecology

  • Article
    | Open Access

    Malnourished children experience a high burden of intestinal pathogens that exacerbate growth stunting, and preventing this pathogen overgrowth has proved challenging. Here the authors show that diet-specific bacterial crossfeeding contributes to the overgrowth of intestinal pathogens during child malnutrition.

    • K. E. Huus
    • , T. T. Hoang
    •  & B. B. Finlay
  • Article
    | Open Access

    Many microbes grow diauxically, utilizing resources one at a time rather than simultaneously. This study developed a minimal model of diauxic microbial communities assembling in a serially diluted culture, providing testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microorganisms.

    • Zihan Wang
    • , Akshit Goyal
    •  & Sergei Maslov
  • Article
    | Open Access

    Here, the authors report quantitative daily gut microbiome variation of individual gut bacterial abundances in healthy individuals, linked to changes in transit time and diet, highlighting the potential need for multiple samplings for microbiome target identification and the development and application of reliable microbiome diagnostics.

    • Doris Vandeputte
    • , Lindsey De Commer
    •  & Jeroen Raes
  • Article
    | Open Access

    The bacterium Vibrio cholerae has caused seven recorded cholera pandemics. The factors responsible for the decline of 6th pandemic classical biotype strains are not well understood. Here, Kostiuk et al. propose that classical strains underwent sequential mutations in type-six secretion system genes that disadvantaged them when confronted with 7th pandemic El Tor biotype strains.

    • Benjamin Kostiuk
    • , Francis J. Santoriello
    •  & Stefan Pukatzki
  • Article
    | Open Access

    Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and has been shown to constitute a multifunctional epigenetic system. Despite a variety of advantages for hosting dnd systems, these systems are surprisingly distributed sporadically among contemporary microbial genomes. To address this ecological paradox, Jian et al. systematically investigated the occurrence and phylogeny of dnd systems in prokaryotes, and provided evidence to suggest that dnd systems have originated in ancient Cyanobacteria (probably Nostocales) after the Great Oxygenation Event.

    • Huahua Jian
    • , Guanpeng Xu
    •  & Xiang Xiao
  • Article
    | Open Access

    Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics in comparison to seasonal and lifetime processes remains unknown. This study of gut bacterial dynamics in wild meerkats over a 20-year period finds that diurnal oscillations in bacterial load and composition eclipse seasonal and lifetime dynamics.

    • Alice Risely
    • , Kerstin Wilhelm
    •  & Simone Sommer
  • Article
    | Open Access

    Here, the authors profile the taxonomic composition and genetic potential of the gut microbiome of children with food or respiratory allergies and find that the gut metagenome of these patients is characterized by higher proinflammatory potential and reduced capacity of degrading complex polysaccharides, with Ruminococcus gnavus playing a central role.

    • Francesca De Filippis
    • , Lorella Paparo
    •  & Roberto Berni Canani
  • Article
    | Open Access

    Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.

    • Joanne B. Emerson
    • , Ruth K. Varner
    •  & Virginia I. Rich
  • Article
    | Open Access

    Legacies of past plant communities are likely to influence plant-soil interactions. Here, the authors report a reciprocal transplant experiment showing that soil microbial legacies shaped by previous plants persist for soil fungi and root endophytes but can be reversed by a next generation of plants for soil bacteria.

    • S. Emilia Hannula
    • , Robin Heinen
    •  & T. Martijn Bezemer
  • Article
    | Open Access

    Studying the role of predator–prey interactions in food-web stability and species coexistence in the environment is arduous. Here, Cohen et al. use a combination of community and single-cell analyses to show that bacterial predators can regulate prey populations in the species-rich environments of wastewater treatment plants.

    • Yossi Cohen
    • , Zohar Pasternak
    •  & Edouard Jurkevitch
  • Article
    | Open Access

    Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.

    • Kara Martin
    • , Katrin Schmidt
    •  & Thomas Mock
  • Article
    | Open Access

    Activated sludge (AS) systems in wastewater treatment plants (WWTPs) contain high concentration of viruses. Here, the authors apply a systematic metagenomic pipeline and retrieve a catalogue of around 50,000 prokaryotic viruses from samples of six WWTPs, revealing a large and uncharacterized viral diversity in AS communities.

    • Yiqiang Chen
    • , Yulin Wang
    •  & Tong Zhang
  • Article
    | Open Access

    Biodiversity-ecosystem functioning relationships may vary with climate. Here, the authors study relationships of plant and soil microbial diversity with soil nutrient multifunctionality in 130 dryland sites in China, finding a shift towards greater importance of soil microbial diversity in arid conditions.

    • Weigang Hu
    • , Jinzhi Ran
    •  & Jianming Deng
  • Article
    | Open Access

    The biology of the archaeal phylum Woesearchaeota is poorly understood due to the lack of cultured isolates. Here, the authors analyze datasets of Woesearchaeota 16 S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities.

    • Wen-Cong Huang
    • , Yang Liu
    •  & Meng Li
  • Article
    | Open Access

    Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.

    • Janina Rahlff
    • , Victoria Turzynski
    •  & Alexander J. Probst
  • Article
    | Open Access

    How acute deoxygenation events affect tropical marine ecosystems remains poorly understood. This study integrates analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered a shallow tropical coral reef ecosystem in the Caribbean.

    • Maggie D. Johnson
    • , Jarrod J. Scott
    •  & Andrew H. Altieri
  • Article
    | Open Access

    Chlamydiae are strictly intracellular bacteria that exist in a wide variety of environments but the diversity of the phylum is not well described. Here, the authors analyze 82 metagenome-assembled genomes, identify seven new families, and describe genomic signals of metabolic diversity.

    • Stephan Köstlbacher
    • , Astrid Collingro
    •  & Matthias Horn
  • Article
    | Open Access

    The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems.

    • Bram W. Stone
    • , Junhui Li
    •  & Bruce A. Hungate
  • Article
    | Open Access

    Microbiomes designed with predictable functions could enable broad applications in health, agriculture and bioprocessing. Here the authors use a model-guided approach to design diverse synthetic human gut communities for production of the health-relevant metabolite butyrate.

    • Ryan L. Clark
    • , Bryce M. Connors
    •  & Ophelia S. Venturelli
  • Article
    | Open Access

    The Candidate Phyla Radiation (CPR) constitutes a large group of bacterial lineages with small cell sizes and limited biosynthetic capabilities. Here, Moreira et al. study the biology and genome of Vampirococcus lugosii, an epibiotic parasite of other bacteria, supporting parasitism as a common lifestyle of CPR bacteria.

    • David Moreira
    • , Yvan Zivanovic
    •  & Purificación López-García
  • Article
    | Open Access

    Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.

    • Valerie De Anda
    • , Lin-Xing Chen
    •  & Brett J. Baker
  • Article
    | Open Access

    How microbial community properties change under increasingly complex combinations of resources remains unclear. Here, the authors studied hundreds of synthetic consortia to identify the factors that govern how growth and taxonomic diversity scale with environmental complexity.

    • Alan R. Pacheco
    • , Melisa L. Osborne
    •  & Daniel Segrè
  • Article
    | Open Access

    There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.

    • Claire E. Couch
    • , Keaton Stagaman
    •  & Anna E. Jolles
  • Article
    | Open Access

    Extracting functional information from 16S rRNA data surveys would provide a valuable tool for large-scale functional ecology. Here, the authors use PICRUSt2 to infer metabolic functions from bacterial marker gene data across the South Pacific Ocean, and compare them with rate data, biomass estimators and predictions based on shotgun metagenomes.

    • Eric J. Raes
    • , Kristen Karsh
    •  & Anya M. Waite
  • Article
    | Open Access

    Here, the authors combine 16 S rRNA sequencing, culture and bioinformatics to profile the microbiome in 234 serial bronchoalveolar lavage samples from 64 lung transplant recipients collected over 49-months and identify distinct compositional states, termed pneumotypes, linked to current health status, and establish a collection of primary lung bacterial isolates, LuMiCol.

    • Sudip Das
    • , Eric Bernasconi
    •  & Laurent P. Nicod
  • Article
    | Open Access

    There is much uncertainty on the response of soil microbial communities to warming, particularly in the subsoil. Here, the authors investigate microbial community and metabolism response to 4.5 years of whole-profile soil warming, finding depth-dependent effects and elevated subsoil microbial respiration.

    • Nicholas C. Dove
    • , Margaret S. Torn
    •  & Neslihan Taş
  • Article
    | Open Access

    It was thought that marine cyanobacteria drifted randomly in the water column. Here the authors show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and retain optimal positions in the water column, as well as evade predation by grazers.

    • Maria del Mar Aguilo-Ferretjans
    • , Rafael Bosch
    •  & Joseph A. Christie-Oleza
  • Article
    | Open Access

    Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.

    • Felipe Senne de Oliveira Lino
    • , Djordje Bajic
    •  & Morten Otto Alexander Sommer
  • Article
    | Open Access

    Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. Here, the authors propose an ecology-based computational method to predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome.

    • Akshit Goyal
    • , Tong Wang
    •  & Sergei Maslov
  • Article
    | Open Access

    Here, the authors present a pig integrated gene catalog and metagenome-assembled genomes, which they construct from swine gut microbiomes spanning various ages, sexes, breeds, geographical locations, domestication, and gut locations by metagenomic sequencing, providing expanded resources for pig microbiome studies.

    • Congying Chen
    • , Yunyan Zhou
    •  & Lusheng Huang
  • Article
    | Open Access

    The spatial arrangement of bacterial strains and species within microbial communities is considered crucial for their ecology. Here, Krishna Kumar et al. use a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array, and show that micron-scale changes in spatial distributions can drive major shifts in ecology.

    • Ravinash Krishna Kumar
    • , Thomas A. Meiller-Legrand
    •  & Kevin R. Foster
  • Article
    | Open Access

    Soil organic matter (SOM) is a huge sink of carbon, but the varied flux dynamics are challenging to predict. Here, the authors present a new model with the complexities of SOM cycling, including parameters for substrate accessibility, microbe diversity, and enzymatic substrate depolymerization.

    • Julien Sainte-Marie
    • , Matthieu Barrandon
    •  & Delphine Derrien
  • Article
    | Open Access

    In naturally occurring microbial systems, there is a positive relationship between species diversity and productivity of the community. Here the authors perform model selection to find potential amensal interactions that yield robust stable synthetic microbial consortia.

    • Behzad D. Karkaria
    • , Alex J. H. Fedorec
    •  & Chris P. Barnes
  • Article
    | Open Access

    Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.

    • Sarah P. Hammarlund
    • , Tomáš Gedeon
    •  & William R. Harcombe
  • Article
    | Open Access

    Bacteria can use type VI secretion systems (T6SSs) to inject toxic effector proteins into adjacent cells, in a contact-dependent manner. Here, the authors provide evidence of contact-independent killing by a T6SS effector that is secreted into the extracellular milieu and then taken up by other bacterial cells.

    • Li Song
    • , Junfeng Pan
    •  & Xihui Shen
  • Article
    | Open Access

    Here, the authors report the results of a longitudinal multi-omics trial of the use of fecal microbiota transplantation (FMT) to ameliorate diarrhea and restore gut microbial composition in 57 growing calves, and find that oral FMT induces alterations in the gut microbiota correlate with the remission of diarrhea and improves the growth performance of the cattle.

    • Hyun Sik Kim
    • , Tae Woong Whon
    •  & Jin-Woo Bae
  • Article
    | Open Access

    It is unclear whether body size affects community assembly mechanisms of soil biota. Here, the authors analyse soil microbial and nematode communities sampled along a 4000-km transect in China and global soil microbiome data to show that bacterial assembly is governed by high dispersal, whereas larger taxa are more influenced by deterministic processes.

    • Lu Luan
    • , Yuji Jiang
    •  & Bo Sun
  • Article
    | Open Access

    The maintenance of ecological diversity depends on the strength and direction of competitive interactions, but these interactions are difficult to study in microbial communities. Here the authors use engineered E. coli strains to show that competitively weak strains can persist when pairwise interactions are asymmetrical.

    • Michael J. Liao
    • , Arianna Miano
    •  & Jeff Hasty
  • Perspective
    | Open Access

    Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.

    • Emily J. Zakem
    • , Martin F. Polz
    •  & Michael J. Follows
  • Article
    | Open Access

    Starvation induces cell aggregation and formation of spore-containing fruiting bodies in the bacterium Myxococcus xanthus. Here, the authors show that a different myxobacterial species produces a compound that inhibits the development of fruiting bodies in M. xanthus, by affecting the function of histidine kinases and major regulators.

    • Francisco Javier Marcos-Torres
    • , Carsten Volz
    •  & Rolf Müller
  • Article
    | Open Access

    Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

    • Malte Herold
    • , Susana Martínez Arbas
    •  & Paul Wilmes
  • Article
    | Open Access

    Soil-borne fungal pathogens use chemotropism and extracellular pH alkalinisation to reach and penetrate plant roots. Here, Palmieri et al. show that soil endophytic bacteria swim along fungal hyphae to colonize plant roots and protect host plants by modulating the pH of the rhizosphere.

    • Davide Palmieri
    • , Stefania Vitale
    •  & David Turrà
  • Article
    | Open Access

    Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

    • Shingo Miyauchi
    • , Enikő Kiss
    •  & Francis M. Martin