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  1. Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with ant...

    Authors: Yuri Pinheiro Alves de Souza, Michael Schloter, Wolfgang Weisser, Yuanyuan Huang and Stefanie Schulz
    Citation: Environmental Microbiome 2024 19:11
  2. Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a s...

    Authors: M. Meyneng, H. Lemonnier, R. Le Gendre, G. Plougoulen, F. Antypas, D. Ansquer, J. Serghine, S. Schmitt and R. Siano
    Citation: Environmental Microbiome 2024 19:10
  3. Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, l...

    Authors: Timothy M. Ghaly, Amaranta Focardi, Liam D. H. Elbourne, Brodie Sutcliffe, William F. Humphreys, Paul R. Jaschke, Sasha G. Tetu and Ian T. Paulsen
    Citation: Environmental Microbiome 2024 19:9
  4. Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining eco...

    Authors: Lenka Mészárošová, Eliška Kuťáková, Petr Kohout, Zuzana Münzbergová and Petr Baldrian
    Citation: Environmental Microbiome 2024 19:8
  5. Bilberry (Vaccinium myrtillus L.) is one of the most important economic and natural resources in Northern Europe. Despite its importance, the endophytic fungal community of the fruits has rarely been investigated...

    Authors: Minh-Phuong Nguyen, Kaisa Lehosmaa, Katalin Toth, Janne J. Koskimäki, Hely Häggman and Anna Maria Pirttilä
    Citation: Environmental Microbiome 2024 19:7
  6. Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. ...

    Authors: Jinchang Liang, Chengjian Wei, Xueru Song, Rui Wang, Heli Shi, Jun Tan, Dejie Cheng, Wenjing Wang and Xiaoqiang Wang
    Citation: Environmental Microbiome 2024 19:6
  7. Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys ov...

    Authors: Marko Terzin, Patrick W. Laffy, Steven Robbins, Yun Kit Yeoh, Pedro R. Frade, Bettina Glasl, Nicole S. Webster and David G. Bourne
    Citation: Environmental Microbiome 2024 19:5
  8. Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitorin...

    Authors: Faizan Saleem, Enze Li, Thomas A. Edge, Kevin L. Tran and Herb E. Schellhorn
    Citation: Environmental Microbiome 2024 19:4
  9. As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural...

    Authors: Wenqian Wang, Dongmei Li, Xiaoqian Qiu, Jinshui Yang, Liang Liu, Entao Wang and Hongli Yuan
    Citation: Environmental Microbiome 2024 19:2
  10. The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorgan...

    Authors: Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, Gabriele Ghiotto, Balázs Kakuk, Maria Silvia Morlino, Arianna Basile, Guido Zampieri, Laura Treu and Stefano Campanaro
    Citation: Environmental Microbiome 2024 19:1
  11. The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the i...

    Authors: Tamara Megan Huete-Stauffer, Ramiro Logares, Mohd Ikram Ansari, Anders Røstad, Maria Lluch Calleja and Xosé Anxelu G. Morán
    Citation: Environmental Microbiome 2023 18:87
  12. Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological st...

    Authors: Ashley M. Dungan, Laura Geissler, Amanda S. Williams, Cecilie Ravn Gotze, Emily C. Flynn, Linda L. Blackall and Madeleine J. H. van Oppen
    Citation: Environmental Microbiome 2023 18:86
  13. Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits o...

    Authors: Lilian S. Abreu Soares Costa, Mírian Rabelo de Faria, Josiane Barros Chiaramonte, Lucas W. Mendes, Edis Sepo, Mattias de Hollander, José Maurício Cunha Fernandes, Víctor J. Carrión, Wagner Bettiol, Tim H. Mauchline, Jos M. Raaijmakers and Rodrigo Mendes
    Citation: Environmental Microbiome 2023 18:85
  14. Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated acros...

    Authors: Joel F. Swift, Zoë Migicovsky, Grace E. Trello and Allison J. Miller
    Citation: Environmental Microbiome 2023 18:84
  15. The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora...

    Authors: Jie Li, Yiyang Zou, Qiqi Li, Jian Zhang, David G. Bourne, Yuanjiao Lyu, Cong Liu and Si Zhang
    Citation: Environmental Microbiome 2023 18:83
  16. Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities....

    Authors: Natalia Gogoleva, Olga Chervyatsova, Alexander Balkin, Lyudmila Kuzmina, Elena Shagimardanova, Daria Kiseleva and Yuri Gogolev
    Citation: Environmental Microbiome 2023 18:82
  17. Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as...

    Authors: Osiel S. Gonçalves, Christopher J. Creevey and Mateus F. Santana
    Citation: Environmental Microbiome 2023 18:81
  18. Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beet...

    Authors: Oana Teodora Moldovan, Alyssa A. Carrell, Paul-Adrian Bulzu, Erika Levei, Ruxandra Bucur, Cristian Sitar, Luchiana Faur, Ionuț Cornel Mirea, Marin Șenilă, Oana Cadar and Mircea Podar
    Citation: Environmental Microbiome 2023 18:80
  19. Lichens are symbiotic organisms composed of a fungus and a photosynthetic partner, which are key ecological bioindicators due to their sensitivity to environmental changes. The endolichenic fungi (ELF) living ...

    Authors: Jiho Yang, Jung-Jae Woo, Wonyong Kim, Seung-Yoon Oh and Jae-Seoun Hur
    Citation: Environmental Microbiome 2023 18:79
  20. Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant’s defens...

    Authors: Xinan Li, Chao Wang, Xun Zhu, Vardis Ntoukakis, Tomislav Cernava and Decai Jin
    Citation: Environmental Microbiome 2023 18:78
  21. Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, virus...

    Authors: Wenbin Zhao, Xing Chen, Ronghua Liu, Peng Tian, Wentao Niu, Xiao-Hua Zhang, Jiwen Liu and Xiaolei Wang
    Citation: Environmental Microbiome 2023 18:77
  22. Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling peri...

    Authors: Xuya Hu, Yujie Huang, Gaoke Gu, Hanjing Hu, Huizhen Yan, Huajun Zhang, Rui Zhang, Demin Zhang and Kai Wang
    Citation: Environmental Microbiome 2023 18:75
  23. Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remedia...

    Authors: Martina Kracmarova-Farren, Jakub Papik, Ondrej Uhlik, John Freeman, Andrea Foster, Mary-Cathrine Leewis and Courtney Creamer
    Citation: Environmental Microbiome 2023 18:74
  24. Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are kn...

    Authors: Jiho Yang, Jung-Jae Woo, Seung-Yoon Oh, Wonyong Kim and Jae-Seoun Hur
    Citation: Environmental Microbiome 2023 18:73
  25. Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited numbe...

    Authors: Ziva Louisson, Louis Ranjard, Hannah L. Buckley, Bradley S. Case and Gavin Lear
    Citation: Environmental Microbiome 2023 18:71
  26. Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with...

    Authors: Romie Tignat-Perrier, Jeroen A. J. M. van de Water, Denis Allemand and Christine Ferrier-Pagès
    Citation: Environmental Microbiome 2023 18:70
  27. The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agri...

    Authors: Dámaris Núñez-Gómez, Pablo Melgarejo, Juan José Martínez-Nicolás, Francisca Hernández, Rafael Martínez-Font, Vicente Lidón and Pilar Legua
    Citation: Environmental Microbiome 2023 18:69
  28. Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infe...

    Authors: Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Edis Sepo, Ruth Gómez Expósito, Alisson Fernando Chiorato, Rodrigo Mendes, Siu Mui Tsai and Victor J Carrión
    Citation: Environmental Microbiome 2023 18:68
  29. The Kuril–Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communi...

    Authors: Susanna Gorrasi, Andrea Franzetti, Angelika Brandt, Ulrike Minzlaff, Marcella Pasqualetti and Massimiliano Fenice
    Citation: Environmental Microbiome 2023 18:67
  30. The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and inform...

    Authors: Ida G. Pantoja-Feliciano De Goodfellow, Richard Agans, Robyn Barbato, Sophie Colston, Michael S. Goodson, Rasha Hammamieh, Kristy Hentchel, Robert Jones, J. Philip Karl, Robert Kokoska, Dagmar H. Leary, Camilla Mauzy, Kenneth Racicot, Blake W. Stamps, Vanessa Varaljay and Jason W. Soares
    Citation: Environmental Microbiome 2023 18:66
  31. A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composit...

    Authors: Kyle Hartman, Marc W. Schmid, Natacha Bodenhausen, S. Franz Bender, Alain Y. Valzano-Held, Klaus Schlaeppi and Marcel G.A. van der Heijden
    Citation: Environmental Microbiome 2023 18:65
  32. Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more in...

    Authors: Zaki Saati-Santamaría, Rocío Vicentefranqueira, Miroslav Kolařik, Raúl Rivas and Paula García-Fraile
    Citation: Environmental Microbiome 2023 18:64
  33. The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microb...

    Authors: Adrian Wolfgang, Ayco J. M. Tack, Gabriele Berg and Ahmed Abdelfattah
    Citation: Environmental Microbiome 2023 18:63
  34. Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the...

    Authors: Vera Hesen, Yvet Boele, Tanja Bakx-Schotman, Femke van Beersum, Ciska Raaijmakers, Ben Scheres, Viola Willemsen and Wim H. van der Putten
    Citation: Environmental Microbiome 2023 18:62
  35. Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with curren...

    Authors: Rafael Bargiela, Aleksei A. Korzhenkov, Owen A. McIntosh, Stepan V. Toshchakov, Mikhail M. Yakimov, Peter N. Golyshin and Olga V. Golyshina
    Citation: Environmental Microbiome 2023 18:61
  36. Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial d...

    Authors: Dev Paudel, Liping Wang, Ravin Poudel, Janam P Acharya, Samantha Victores, Cleber Henrique Lopes de Souza, Esteban Rios and Jianping Wang
    Citation: Environmental Microbiome 2023 18:60
  37. In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, ...

    Authors: Marie Colette, Linda Guentas, Luc Della Patrona, Dominique Ansquer and Nolwenn Callac
    Citation: Environmental Microbiome 2023 18:58
  38. The phyllosphere mycobiome plays a crucial role in plant fitness and ecosystem functions. The complex microbial ecological networks (MEN) formed by these fungi remain poorly understood, particularly with regar...

    Authors: Guozhuang Zhang, Liping Shi, Congsheng Liu, Renjun Mao, Bing Xia, Zhixin Huang, Xiuye Wei, Lixuan Wu, Yuqing Zheng, Guangfei Wei, Jia Xu, Shuangrong Gao, Shilin Chen and Linlin Dong
    Citation: Environmental Microbiome 2023 18:57
  39. ‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omic...

    Authors: Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin and Magnus Ø. Arntzen
    Citation: Environmental Microbiome 2023 18:56
  40. The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways...

    Authors: Hanna Angstmann, Stefan Pfeiffer, Susanne Kublik, Birte Ehrhardt, Karin Uliczka, Klaus F. Rabe, Thomas Roeder, Christina Wagner, Michael Schloter and Susanne Krauss-Etschmann
    Citation: Environmental Microbiome 2023 18:55
  41. Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze–tha...

    Authors: Ciro Sannino, Weihong Qi, Joel Rüthi, Beat Stierli and Beat Frey
    Citation: Environmental Microbiome 2023 18:54
  42. Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark ...

    Authors: Ezequiel Peral-Aranega, Zaki Saati-Santamaría, Miguel Ayuso-Calles, Martin Kostovčík, Tereza Veselská, Karel Švec, Raúl Rivas, Miroslav Kolařik and Paula García-Fraile
    Citation: Environmental Microbiome 2023 18:53
  43. Marine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Change...

    Authors: Claire E. Lamb and Joy E. M. Watts
    Citation: Environmental Microbiome 2023 18:52
  44. Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is ...

    Authors: Lukas P. Bell-Dereske, Gian Maria Niccolò Benucci, Pedro Beschoren da Costa, Gregory Bonito, Maren L. Friesen, Lisa K. Tiemann and Sarah E. Evans
    Citation: Environmental Microbiome 2023 18:50