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  1. Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits re...

    Authors: Rui Liu, Ruining Cai, Minxiao Wang, Jing Zhang, Huan Zhang, Chaolun Li and Chaomin Sun
    Citation: Environmental Microbiome 2024 19:43
  2. Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly ...

    Authors: Clémentine Lepinay, Tomáš Větrovský, Milan Chytrý, Pavel Dřevojan, Karel Fajmon, Tomáš Cajthaml, Petr Kohout and Petr Baldrian
    Citation: Environmental Microbiome 2024 19:42
  3. To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seep...

    Authors: Narendrakumar M. Chaudhari, Olga M. Pérez-Carrascal, Will A. Overholt, Kai U. Totsche and Kirsten Küsel
    Citation: Environmental Microbiome 2024 19:41
  4. Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less un...

    Authors: Kristina Michl, Christophe David, Benjamin Dumont, Linda-Maria Dimitrova Mårtensson, Frank Rasche, Gabriele Berg and Tomislav Cernava
    Citation: Environmental Microbiome 2024 19:40
  5. Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities wi...

    Authors: Benoit Paix, Elodie van der Valk and Nicole J. de Voogd
    Citation: Environmental Microbiome 2024 19:37
  6. Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured b...

    Authors: Sabrina Ninck, Thomas Klaus, Tatiana V. Kochetkova, Sarah P. Esser, Leonard Sewald, Farnusch Kaschani, Christopher Bräsen, Alexander J. Probst, Ilya V. Kublanov, Bettina Siebers and Markus Kaiser
    Citation: Environmental Microbiome 2024 19:36
  7. Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil ...

    Authors: Michelle Hagen, Rupashree Dass, Cathy Westhues, Jochen Blom, Sebastian J. Schultheiss and Sascha Patz
    Citation: Environmental Microbiome 2024 19:35
  8. Plastic pollution is a severe threat to marine ecosystems. While some microbial enzymes can degrade certain plastics, the ability of the global ocean microbiome to break down diverse environmental plastics rem...

    Authors: Victor Gambarini, Cornelis J. Drost, Joanne M. Kingsbury, Louise Weaver, Olga Pantos, Kim M. Handley and Gavin Lear
    Citation: Environmental Microbiome 2024 19:34
  9. Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness....

    Authors: Caroline Sayuri Nishisaka, João Paulo Ventura, Harsh P. Bais and Rodrigo Mendes
    Citation: Environmental Microbiome 2024 19:33
  10. Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the convers...

    Authors: Paul Benalcazar, Brent Seuradge, Amanda C. Diochon, Randall K. Kolka and Lori A. Phillips
    Citation: Environmental Microbiome 2024 19:32
  11. Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on p...

    Authors: Indranil Mukherjee, Vesna Grujčić, Michaela M. Salcher, Petr Znachor, Jaromír Seďa, Miloslav Devetter, Pavel Rychtecký, Karel Šimek and Tanja Shabarova
    Citation: Environmental Microbiome 2024 19:31
  12. Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the...

    Authors: Sonya R. Erlandson, Patrick M. Ewing, Shannon L. Osborne and R. Michael Lehman
    Citation: Environmental Microbiome 2024 19:30
  13. Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown b...

    Authors: Kok Jun Liew, Saleha Shahar, Mohd Shahir Shamsir, Nawal Binti Shaharuddin, Chee Hung Liang, Kok-Gan Chan, Stephen Brian Pointing, Rajesh Kumar Sani and Kian Mau Goh
    Citation: Environmental Microbiome 2024 19:29
  14. Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of th...

    Authors: Iva Stojan, Danijela Šantić, Cristian Villena-Alemany, Željka Trumbić, Frano Matić, Ana Vrdoljak Tomaš, Ivana Lepen Pleić, Kasia Piwosz, Grozdan Kušpilić, Živana Ninčević Gladan, Stefanija Šestanović and Mladen Šolić
    Citation: Environmental Microbiome 2024 19:28
  15. Plastics pollution and antimicrobial resistance (AMR) are two major environmental threats, but potential connections between plastic associated biofilms, the ‘plastisphere’, and dissemination of AMR genes are ...

    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 and Peter N. Golyshin
    Citation: Environmental Microbiome 2024 19:27
  16. Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining...

    Authors: Jennifer L. Goff, Elizabeth G. Szink, Konnor L. Durrence, Lauren M. Lui, Torben N. Nielsen, Jennifer V. Kuehl, Kristopher A. Hunt, John-Marc Chandonia, Jiawen Huang, Michael P. Thorgersen, Farris L. Poole II, David A. Stahl, Romy Chakraborty, Adam M. Deutschbauer, Adam P. Arkin and Michael W. W. Adams
    Citation: Environmental Microbiome 2024 19:26
  17. Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of e...

    Authors: Daniele Ghezzi, Nicasio Tomás Jiménez-Morillo, Lisa Foschi, Eva Donini, Veronica Chiarini, Jo De Waele, Ana Zélia Miller and Martina Cappelletti
    Citation: Environmental Microbiome 2024 19:25
  18. Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence...

    Authors: Vincent Lailheugue, Romain Darriaut, Joseph Tran, Marine Morel, Elisa Marguerit and Virginie Lauvergeat
    Citation: Environmental Microbiome 2024 19:24
  19. The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To bette...

    Authors: Benjamin J. Wainwright, Josh Leon, Ernie Vilela, K. J. E. Hickman, Jensen Caldwell, Behlee Aimone, Porter Bischoff, Marissa Ohran, Magnolia W. Morelli, Irma S. Arlyza, Onny N. Marwayana and Geoffrey Zahn
    Citation: Environmental Microbiome 2024 19:23
  20. Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene e...

    Authors: Fang Liu, Taewoo Ryu, Timothy Ravasi, Xin Wang, Guangyi Wang and Zhiyong Li
    Citation: Environmental Microbiome 2024 19:22
  21. The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are sub...

    Authors: Yiwei Duan, Andjin Siegenthaler, Andrew K. Skidmore, Anthony A. Chariton, Ivo Laros, Mélody Rousseau and G. Arjen De Groot
    Citation: Environmental Microbiome 2024 19:21
  22. In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow cover...

    Authors: Maraike Probst, Anusha Telagathoti, Edoardo Mandolini and Ursula Peintner
    Citation: Environmental Microbiome 2024 19:20
  23. Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and metic...

    Authors: Niranjana Rose Edwin, Amy Heather Fitzpatrick, Fiona Brennan, Florence Abram and Orla O’Sullivan
    Citation: Environmental Microbiome 2024 19:19
  24. Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an...

    Authors: Sana Romdhane, Sarah Huet, Aymé Spor, David Bru, Marie-Christine Breuil and Laurent Philippot
    Citation: Environmental Microbiome 2024 19:18
  25. The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no...

    Authors: Nuria M. Wentzien, Antonio J. Fernández-González, Antonio Valverde-Corredor, Ana V. Lasa, Pablo J. Villadas, Wisnu Adi Wicaksono, Tomislav Cernava, Gabriele Berg, Manuel Fernández-López and Jesús Mercado-Blanco
    Citation: Environmental Microbiome 2024 19:17
  26. Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat to humankind. The development of methods that allow robust ARG surveill...

    Authors: Lucia Maestre-Carballa, Vicente Navarro-López and Manuel Martinez-Garcia
    Citation: Environmental Microbiome 2024 19:16
  27. Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge micr...

    Authors: Marta Turon, Madeline Ford, Manuel Maldonado, Cèlia Sitjà, Ana Riesgo and Cristina Díez-Vives
    Citation: Environmental Microbiome 2024 19:15
  28. Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pa...

    Authors: Vanessa E. Thomas and Sanjay Antony-Babu
    Citation: Environmental Microbiome 2024 19:14
  29. Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot spr...

    Authors: Xingyun Yi, Kristian Koefoed Brandt, Shudan Xue, Jingjing Peng, Yifei Wang, Meng Li, Ye Deng and Guilan Duan
    Citation: Environmental Microbiome 2024 19:13
  30. Potato seed tubers are colonized and inhabited by soil-borne microbes, that can affect the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational in...

    Authors: Yang Song, Jelle Spooren, Casper D. Jongekrijg, Ellen J. H. H. Manders, Ronnie de Jonge, Corné M. J. Pieterse, Peter A. H. M. Bakker and Roeland L. Berendsen
    Citation: Environmental Microbiome 2024 19:12
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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