Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

JOURNAL ARTICLE published December 2020 in Environmental Microbiome

Research funded by Department of Energy (DE-AC02-05CH11231)

Authors: Briana S. Abraham | Deniz Caglayan | Natalie V. Carrillo | Matthew C. Chapman | Claire T. Hagan | Skye T. Hansen | Ralph O. Jeanty | Alexander A. Klimczak | Marcos J. Klingler | Thomas P. Kutcher | Sydney H. Levy | Angel A. Millard-Bruzos | Thomas B. Moore | David J. Prentice | Matthew E. Prescott | Richard Roehm | Jordan A. Rose | Mulan Yin | Ayumi Hyodo | Kathleen Lail | Christopher Daum | Alicia Clum | Alex Copeland | Rekha Seshadri | Tijana Glavina del Rio | Emiley A. Eloe-Fadrosh | Jonathan B. Benskin

Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling

JOURNAL ARTICLE published December 2022 in Environmental Microbiome

Research funded by National Key R&D Program of China (2019YFE0108500)

Authors: Yajiao Wang | Yu Liu | Yuxing Wu | Nan Wu | Wenwen Liu | Xifeng Wang

Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum

JOURNAL ARTICLE published 16 January 2024 in Environmental Microbiome

Research funded by Major Tobacco Science and Technology Projects (YXYC2022008,110202101054(LS-14)) | Central Public-interest Scientific Institution Basal Research Fund (No. 1610232023018) | Key Laboratory of Tobacco Pest Monitoring & Integrated Management (KLTMMIMT2022-09) | Agricultural Science and Technology Innovation Program of China (ASTIP-TRIC04)

Authors: Jinchang Liang | Chengjian Wei | Xueru Song | Rui Wang | Heli Shi | Jun Tan | Dejie Cheng | Wenjing Wang | Xiaoqiang Wang

Weather in two climatic regions shapes the diversity and drives the structure of fungal endophytic community of bilberry (Vaccinium myrtillus L.) fruit

JOURNAL ARTICLE published 22 January 2024 in Environmental Microbiome

Research funded by Finnish Cultural Foundation (00220726) | Kone Foundation (201806416) | Academy of Finland (343565)

Authors: Minh-Phuong Nguyen | Kaisa Lehosmaa | Katalin Toth | Janne J. Koskimäki | Hely Häggman | Anna Maria Pirttilä

New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

JOURNAL ARTICLE published 28 February 2023 in Environmental Microbiome

Research funded by Mexican National Council for Science and Technology (2018-000061-02EXTF-00218) | NERC (NE/R013462/1)

Authors: Natali Hernandez-Becerra | Lisa Cliffe | Wei Xiu | Christopher Boothman | Jonathan R. Lloyd | Sophie L. Nixon

Evolutionary patterns of archaea predominant in acidic environment

JOURNAL ARTICLE published 18 July 2023 in Environmental Microbiome

Research funded by European Regional Development Fund (N 810280,N 810280,N 810280) | Leverhulme Trust (RPG-2020-190,RPG-2020-190,RPG-2020-190)

Authors: Rafael Bargiela | Aleksei A. Korzhenkov | Owen A. McIntosh | Stepan V. Toshchakov | Mikhail M. Yakimov | Peter N. Golyshin | Olga V. Golyshina

Meeting report of the third annual Tri-Service Microbiome Consortium symposium

JOURNAL ARTICLE published December 2020 in Environmental Microbiome

Authors: J. Philip Karl | Robyn A. Barbato | Laurel A. Doherty | Aarti Gautam | Sarah M. Glaven | Robert J. Kokoska | Dagmar Leary | Rebecca L. Mickol | Matthew A. Perisin | Andrew J. Hoisington | Edward J. Van Opstal | Vanessa Varaljay | Nancy Kelley-Loughnane | Camilla A. Mauzy | Michael S. Goodson | Jason W. Soares

Correction to: Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov

JOURNAL ARTICLE published 7 June 2023 in Environmental Microbiome

Authors: Sahare Kokcha | Ajay Kumar Mishra | Jean-Christophe Lagier | Matthieu Million | Quentin Leroy | Didier Raoult | Pierre-Edouard Fournier

Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere

JOURNAL ARTICLE published 26 August 2021 in Environmental Microbiome

Research funded by Natural Environment Research Council (NE/J009725/1,NE/R000131/1) | European Research Council (694578—IsoMet)

Authors: Lisa Gibson | Andrew T. Crombie | Niall P. McNamara | J. Colin Murrell

Microbial communities colonising plastics during transition from the wastewater treatment plant to marine waters

JOURNAL ARTICLE published 29 April 2024 in Environmental Microbiome

Research funded by Natural Environment Research Council (NE/S004548,NE/S004548,NE/S004548,NE/S004548,NE/S004548,NE/S005501/1,NE/S005501/1,NE/S004548,NE/S004548,NE/S004548) | European Regional Development Fund (81280,81280,81280,81280,81280,81280,81280) | Horizon 2020 Framework Programme (101000327,101000327,101000327)

Authors: Constance L. Tulloch | Rafael Bargiela | Gwion B. Williams | Tatyana N. Chernikova | Benjamin M. Cotterell | Elizabeth M. H. Wellington | Joseph Christie-Oleza | David N. Thomas | Davey L. Jones | Peter N. Golyshin

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics

JOURNAL ARTICLE published 5 March 2022 in Environmental Microbiome

Authors: Gleb Goussarov | Jürgen Claesen | Mohamed Mysara | Ilse Cleenwerck | Natalie Leys | Peter Vandamme | Rob Van Houdt

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

JOURNAL ARTICLE published December 2020 in Environmental Microbiome

Research funded by United States Department of Agriculture-National Institute of Food and Agriculture (2016-68007-25064) | National Science Foundation (1632976)

Authors: Jessica Chopyk | Daniel J. Nasko | Sarah Allard | Anthony Bui | Mihai Pop | Emmanuel F. Mongodin | Amy R. Sapkota

Frequency of occurrence and habitat selection shape the spatial variation in the antibiotic resistome in riverine ecosystems in eastern China

JOURNAL ARTICLE published 2 November 2022 in Environmental Microbiome

Authors: Chunxia Jiang | Haiyang Chen | Hans-Peter Grossart | Quanfa Zhang | Robby Stoks | Yi Zhao | Feng Ju | Wenzhi Liu | Yuyi Yang

Phytoplankton ecology in the early years of a boreal oil sands end pit lake

JOURNAL ARTICLE published 12 January 2024 in Environmental Microbiome

Research funded by Natural Sciences and Engineering Research Council of Canada (CRDPJ 542973-19,CRDPJ 542973-19,CRDPJ 542973-19,CRDPJ 542973-19)

Authors: Chantel C. Furgason | Angela V. Smirnova | Joel B. Dacks | Peter F. Dunfield

Correction to: Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance

JOURNAL ARTICLE published December 2022 in Environmental Microbiome

Authors: Fotios Bekris | Sotirios Vasileiadis | Elena Papadopoulou | Anastasios Samaras | Stefanos Testempasis | Danae Gkizi | Georgia Tavlaki | Aliki Tzima | Epaminondas Paplomatas | Emmanuel Markakis | George Karaoglanidis | Kalliope K. Papadopoulou | Dimitrios G. Karpouzas

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

JOURNAL ARTICLE published December 2020 in Environmental Microbiome

Research funded by N/A (N/A, please see Funding section)

Authors: Renxing Liang | Maggie C. Y. Lau | Evan T. Saitta | Zachary K. Garvin | Tullis C. Onstott

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

JOURNAL ARTICLE published 6 May 2024 in Environmental Microbiome

Research funded by Malaysia Fundamental Research Grant Scheme (FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4,FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4,FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4,FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4,FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4) | UTM QuickWin grant (4J549,4J549) | Singapore Ministry of Education ARC Tier 2 fund (T2EP30123-0028) | National Science Foundation (1736255, 1849206, and 1920954)

Authors: Kok Jun Liew | Saleha Shahar | Mohd Shahir Shamsir | Nawal Binti Shaharuddin | Chee Hung Liang | Kok-Gan Chan | Stephen Brian Pointing | Rajesh Kumar Sani | Kian Mau Goh

Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis

JOURNAL ARTICLE published 8 April 2024 in Environmental Microbiome

Research funded by This work was supported by the National Natural Science Foundation of China (31861143020, 41776138)

Authors: Fang Liu | Taewoo Ryu | Timothy Ravasi | Xin Wang | Guangyi Wang | Zhiyong Li

Endorhizosphere of indigenous succulent halophytes: a valuable resource of plant growth promoting bacteria

JOURNAL ARTICLE published 18 March 2023 in Environmental Microbiome

Research funded by Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja (451-03-47/2023-01/ 200042,451-03-47/2023-01/ 200042,451-03-47/2023-01/200116,451-03-47/2023-01/200116)

Authors: Milica Dragojević | Nada Stankovic | Lidija Djokic | Vera Raičević | Jelena Jovičić-Petrović

Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem

JOURNAL ARTICLE published 17 May 2023 in Environmental Microbiome

Authors: Donald Tchouomo Dondjou | Abdala Gamby Diedhiou | Daouda Mbodj | Marie-Thérèse Mofini | Sarah Pignoly | Cheikh Ndiaye | Issa Diedhiou | Komi Assigbetse | Baboucarr Manneh | Laurent Laplaze | Aboubacry Kane