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  1. Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attemp...

    Authors: William L. King, Sarah C. Richards, Laura M. Kaminsky, Brosi A. Bradley, Jason P. Kaye and Terrence H. Bell
    Citation: Environmental Microbiome 2023 18:7
  2. Río Celeste (“Sky-Blue River”) is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated t...

    Authors: Alejandro Arce-Rodríguez, Eduardo Libby, Erick Castellón, Roberto Avendaño, Juan Carlos Cambronero, Maribel Vargas, Dietmar H. Pieper, Stefan Bertilsson, Max Chavarría and Fernando Puente-Sánchez
    Citation: Environmental Microbiome 2023 18:6
  3. Biting midges (Culicoides spp.) are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. However, little is known about the role of micr...

    Authors: Saraswoti Neupane, Travis Davis, Dana Nayduch and Bethany L. McGregor
    Citation: Environmental Microbiome 2023 18:5
  4. The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbia...

    Authors: Wen-Hui Lian, Osama Abdalla Abdelshafy Mohamad, Lei Dong, Ling-Yu Zhang, Dong Wang, Lan Liu, Ming-Xian Han, Shuai Li, Shuang Wang, André Antunes, Bao-Zhu Fang, Jian-Yu Jiao and Wen-Jun Li
    Citation: Environmental Microbiome 2023 18:4
  5. Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanoba...

    Authors: Jie Zhu, Feng Yang, Kang Du, Zi-Lu Wei, Qing-Fa Wu, Yuxing Chen, Wei-Fang Li, Qiong Li and Cong-Zhao Zhou
    Citation: Environmental Microbiome 2023 18:3
  6. Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technol...

    Authors: Neelakantan Thulasi Devika, Vinaya Kumar Katneni, Ashok Kumar Jangam, Panjan Nathamuni Suganya, Mudagandur Shashi Shekhar and Karingalakkandy Poochirian Jithendran
    Citation: Environmental Microbiome 2023 18:2
  7. Honeybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. ...

    Authors: Lorenzo A. Santorelli, Toby Wilkinson, Ronke Abdulmalik, Yuma Rai, Christopher J. Creevey, Sharon Huws and Jorge Gutierrez-Merino
    Citation: Environmental Microbiome 2023 18:1
  8. Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experimen...

    Authors: Gwynne Á. Mhuireach, Ashkaan K. Fahimipour, Roo Vandegrift, Mario E. Muscarella, Roxana Hickey, Ashley C. Bateman, Kevin G. Van Den Wymelenberg and Brendan J. M. Bohannan
    Citation: Environmental Microbiome 2022 17:61
  9. Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a ...

    Authors: Maria A. Sierra, Krista A. Ryon, Braden T. Tierney, Jonathan Foox, Chandrima Bhattacharya, Evan Afshin, Daniel Butler, Stefan J. Green, W. Kelley Thomas, Jordan Ramsdell, Nathan J. Bivens, Ken McGrath, Christopher E. Mason and Scott W. Tighe
    Citation: Environmental Microbiome 2022 17:60
  10. Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy eff...

    Authors: Xiaoping Li, Victoria Skillman, Jeremiah Dung and Kenneth Frost
    Citation: Environmental Microbiome 2022 17:59
  11. Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches ex...

    Authors: Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li…
    Citation: Environmental Microbiome 2022 17:58
  12. Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Meta...

    Authors: Muhammad Kabiru Nata’ala, Anderson P. Avila Santos, Jonas Coelho Kasmanas, Alexander Bartholomäus, João Pedro Saraiva, Sandra Godinho Silva, Tina Keller-Costa, Rodrigo Costa, Newton C. M. Gomes, André Carlos Ponce de Leon Ferreira de Carvalho, Peter F. Stadler, Danilo Sipoli Sanches and Ulisses Nunes da Rocha
    Citation: Environmental Microbiome 2022 17:57
  13. Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbio...

    Authors: Ankush Chandel, Ross Mann, Jatinder Kaur, Ian Tannenbaum, Sally Norton, Jacqueline Edwards, German Spangenberg and Timothy Sawbridge
    Citation: Environmental Microbiome 2022 17:56
  14. Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the m...

    Authors: Jungsoo Park, Katherine Davis, Geneviève Lajoie and Laura Wegener Parfrey
    Citation: Environmental Microbiome 2022 17:55
  15. In the ice-free area of maritime Antarctica, fungi are the essential functioning group in terrestrial and marine ecosystems. Until now, no study has been conducted to comprehensively assess fungal communities ...

    Authors: Tao Zhang, Dong Yan, Zhongqiang Ji, Xiufei Chen and Liyan Yu
    Citation: Environmental Microbiome 2022 17:54
  16. Riverine ecosystems are one of the most important reservoirs of antibiotic resistance genes (ARGs) in the environment, but the occurrence and controlling factors of ARG distribution in different habitats of ri...

    Authors: Chunxia Jiang, Haiyang Chen, Hans-Peter Grossart, Quanfa Zhang, Robby Stoks, Yi Zhao, Feng Ju, Wenzhi Liu and Yuyi Yang
    Citation: Environmental Microbiome 2022 17:53
  17. Rhizosphere fungi and endophytic fungi play key roles in plant growth and development; however, their role in the growth of Epimedium koreanum Nakai at different stages remains unclear. Here, we used the Illumina...

    Authors: Chen Jiawen, Wu Yuan, Zhuang Xin, Guo Junjie, Hu Xing and Xiao Jinglei
    Citation: Environmental Microbiome 2022 17:52
  18. The rhizosphere is a nexus for plant–microbe interactions and, as a host-structured environment, a location of high activity for distinct microbes and plant species. Although our insights into this habitat hav...

    Authors: Suzanne M. Fleishman, David M. Eissenstat, Terrence H. Bell and Michela Centinari
    Citation: Environmental Microbiome 2022 17:51
  19. The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiome...

    Authors: Lene Lange, Gabriele Berg, Tomislav Cernava, Marie-Christine Champomier-Vergès, Trevor Charles, Luca Cocolin, Paul Cotter, Kathleen D’Hondt, Tanja Kostic, Emmanuelle Maguin, Thulani Makhalanyane, Annelein Meisner, Matthew Ryan, George Seghal Kiran, Rafael Soares de Souza, Yolanda Sanz…
    Citation: Environmental Microbiome 2022 17:50
  20. The nitrogenous compound deposited from the atmosphere to the soil is complex, but most field experiments mimic nitrogen deposition with the acid NH4NO3 alone. Thus, whether the acid and non-acid nitrogenous comp...

    Authors: Tingting Li, Zijia Zhang, Yiping Ma, Yuqian Song, Guojiao Yang, Xingguo Han and Ximei Zhang
    Citation: Environmental Microbiome 2022 17:49
  21. The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs...

    Authors: Tereza Smrhova, Kunal Jani, Petr Pajer, Gabriela Kapinusova, Tomas Vylita, Jachym Suman, Michal Strejcek and Ondrej Uhlik
    Citation: Environmental Microbiome 2022 17:48
  22. The entomopathogenic Beauveria bassiana is a popular fungus used to control the Japanese pine sawyer, Monochamus alternatus Hope, the key vector of pine wood nematode (Bursaphelenchus xylophilus) that is the caus...

    Authors: Jundan Deng, Weikang Xu, Guochang Lv, Hang Yuan, Qing-He Zhang, Jacob D. Wickham, Letian Xu and Longwa Zhang
    Citation: Environmental Microbiome 2022 17:47
  23. Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints b...

    Authors: Henry W. G. Birt, Anthony B. Pattison, Adam Skarshewski, Jeff Daniells, Anil Raghavendra and Paul G. Dennis
    Citation: Environmental Microbiome 2022 17:46
  24. Biochar is considered to be a possible means of carbon sequestration to alleviate climate change. However, the dynamics of the microbial community during wood decomposition after biochar application remain poo...

    Authors: Zhao-lei Qu, Xiao-li Li, Yan Ge, Marjo Palviainen, Xuan Zhou, Jussi Heinonsalo, Frank Berninger, Jukka Pumpanen, Kajar Köster and Hui Sun
    Citation: Environmental Microbiome 2022 17:45
  25. Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current und...

    Authors: Iulia Chiciudean, Giancarlo Russo, Diana Felicia Bogdan, Erika Andrea Levei, Luchiana Faur, Alexandra Hillebrand-Voiculescu, Oana Teodora Moldovan and Horia Leonard Banciu
    Citation: Environmental Microbiome 2022 17:44
  26. Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by ...

    Authors: Yangyang Jia, Shengguo Zhao, Wenjie Guo, Ling Peng, Fang Zhao, Lushan Wang, Guangyi Fan, Yuanfang Zhu, Dayou Xu, Guilin Liu, Ruoqing Wang, Xiaodong Fang, He Zhang, Karsten Kristiansen, Wenwei Zhang and Jianwei Chen
    Citation: Environmental Microbiome 2022 17:43
  27. Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal ma...

    Authors: Tianlei Qiu, Linhe Huo, Yajie Guo, Min Gao, Guoliang Wang, Dong Hu, Cheng Li, Zhanwu Wang, Guiming Liu and Xuming Wang
    Citation: Environmental Microbiome 2022 17:42
  28. Subarctic regions are particularly vulnerable to climate change, yet little is known about nutrient availability and biodiversity of their cave ecosystems. Such knowledge is crucial for predicting the vulnerab...

    Authors: Ana Sofia Reboleira, Kasun H. Bodawatta, Nynne M. R. Ravn, Stein-Erik Lauritzen, Rannveig Øvrevik Skoglund, Michael Poulsen, Anders Michelsen and Knud Andreas Jønsson
    Citation: Environmental Microbiome 2022 17:41
  29. The genus Tetracladium De Wild. (Ascomycota) has been traditionally regarded as a group of Ingoldian fungi or aquatic hyphomycetes—a polyphyletic group of phylogenetically diverse fungi which grow on decaying lea...

    Authors: Anna Lazar, Ryan M. Mushinski and Gary D. Bending
    Citation: Environmental Microbiome 2022 17:40
  30. Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing...

    Authors: Alejandro Palomo, Daniela Azevedo, María Touceda-Suárez, Carlos Domingo-Félez, A. Gizem Mutlu, Arnaud Dechesne, Yulin Wang, Tong Zhang and Barth F. Smets
    Citation: Environmental Microbiome 2022 17:39
  31. The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root ...

    Authors: Benoît Perez-Lamarque, Rémi Petrolli, Christine Strullu-Derrien, Dominique Strasberg, Hélène Morlon, Marc-André Selosse and Florent Martos
    Citation: Environmental Microbiome 2022 17:38
  32. Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic org...

    Authors: Javier Edo Varg, David Outomuro, Warren Kunce, Lukas Kuehrer, Richard Svanbäck and Frank Johansson
    Citation: Environmental Microbiome 2022 17:36
  33. Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ...

    Authors: Saranya Kanukollu, Rainer Remus, Alexander Martin Rücker, Caroline Buchen-Tschiskale, Mathias Hoffmann and Steffen Kolb
    Citation: Environmental Microbiome 2022 17:35
  34. Understanding the factors that influence microbes’ environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature an...

    Authors: John L. Darcy, Anthony S. Amend, Sean O. I. Swift, Pacifica S. Sommers and Catherine A. Lozupone
    Citation: Environmental Microbiome 2022 17:34
  35. Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata i...

    Authors: Tomislav Cernava, Daria Rybakova, François Buscot, Thomas Clavel, Alice Carolyn McHardy, Fernando Meyer, Folker Meyer, Jörg Overmann, Bärbel Stecher, Angela Sessitsch, Michael Schloter and Gabriele Berg
    Citation: Environmental Microbiome 2022 17:33
  36. It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic envi...

    Authors: Sujata Dey, Ajaya Kumar Rout, Bijay Kumar Behera and Koushik Ghosh
    Citation: Environmental Microbiome 2022 17:32
  37. In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling ...

    Authors: Igor S. Pessi, Sirja Viitamäki, Anna-Maria Virkkala, Eeva Eronen-Rasimus, Tom O. Delmont, Maija E. Marushchak, Miska Luoto and Jenni Hultman
    Citation: Environmental Microbiome 2022 17:30
  38. Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities ...

    Authors: Mengjiao Li, Lan Hong, Wanhui Ye, Zhangming Wang and Hao Shen
    Citation: Environmental Microbiome 2022 17:29
  39. With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicr...

    Authors: Kuleshwar Prasad Sahu, A. Kumar, K. Sakthivel, Bhaskar Reddy, Mukesh Kumar, Asharani Patel, Neelam Sheoran, Subbaiyan Gopalakrishnan, Ganesan Prakash, Rajeev Rathour and R. K. Gautam
    Citation: Environmental Microbiome 2022 17:28
  40. While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evalu...

    Authors: Xue Zhu, Lei Ji, Mingyue Cheng, Huimin Wei, Zhi Wang and Kang Ning
    Citation: Environmental Microbiome 2022 17:27
  41. Metal(loid)s can promote the spread and enrichment of antibiotic resistance genes (ARGs) in the environment through a co-selection effect. However, it remains unclear whether exposure of microorganisms to vary...

    Authors: Fang-Fang Wang, Guo-Ping Liu, Fan Zhang, Zong-Ming Li, Xiao-Lin Yang, Chao-Dong Yang, Jian-Lin Shen, Ji-Zheng He, B. Larry Li and Jian-Guo Zeng
    Citation: Environmental Microbiome 2022 17:26
  42. Microorganisms are known to be important drivers of biogeochemical cycling in soil and hence could act as a proxy informing on soil conditions in ecosystems. Identifying microbiomes indicative for soil fertili...

    Authors: Jianwei Zhang, Jan Dolfing, Wenjing Liu, Ruirui Chen, Jiabao Zhang, Xiangui Lin and Youzhi Feng
    Citation: Environmental Microbiome 2022 17:25
  43. Chloromethane (CH3Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH3Cl sources have...

    Authors: Eileen Kröber, Saranya Kanukollu, Sonja Wende, Françoise Bringel and Steffen Kolb
    Citation: Environmental Microbiome 2022 17:24
  44. Glycyrrhiza uralensis Fisch. is an important, perennial medicinal plant whose root microbiome is considered to play an important role in promoting accumulation of effective medicinal ingredients (liquiritin and g...

    Authors: Chaoyun Chen, Chaofang Zhong, Xi Gao, Chongyang Tan, Hong Bai and Kang Ning
    Citation: Environmental Microbiome 2022 17:23
  45. Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth’s primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that ar...

    Authors: Anders K. Krabberød, Ina M. Deutschmann, Marit F. M. Bjorbækmo, Vanessa Balagué, Caterina R. Giner, Isabel Ferrera, Esther Garcés, Ramon Massana, Josep M. Gasol and Ramiro Logares
    Citation: Environmental Microbiome 2022 17:22
  46. Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two ...

    Authors: Expedito Olimi, Peter Kusstatscher, Wisnu Adi Wicaksono, Ahmed Abdelfattah, Tomislav Cernava and Gabriele Berg
    Citation: Environmental Microbiome 2022 17:21
  47. Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m be...

    Authors: Liuqing He, Xinyu Huang, Guoqing Zhang, Ling Yuan, Enhui Shen, Lu Zhang, Xiao-Hua Zhang, Tong Zhang, Liang Tao and Feng Ju
    Citation: Environmental Microbiome 2022 17:19