# Topics and Trends in Most Cited Microbial Community Ecology and Physiology Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/microbial-community-ecology-and-physiology/2026*

## What topics and trends defined most-cited Microbial Community Ecology and Physiology research in the Class of 2026?

Microbial carbon use efficiency dominates the 2026 cohort, driven by a growing focus on mechanistic soil ecology. High-throughput tools like metagenomics and 16S sequencing remain foundational, while specialized topics like network complexity and salt stress showed the largest year-over-year gains in citation share.

## At a glance

| Fact | Value |
| --- | --- |
| Field | Microbial Community Ecology and Physiology |
| Cohort label | Class of 2026 (2024 publications) |
| Papers analyzed | 8739 |
| Papers ranked | 20 |
| Top topics in ranked papers | Microbial carbon use efficiency, 16S rRNA gene sequencing, Metagenomics, Microbial necromass |
| Publication window | Jan 1, 2024 – Dec 31, 2024 |
| Eligibility | Research articles; reviews excluded |
| Citation window | 18 months post-publication |
| 18m citation range | 78–203 |
| Data source | OpenAlex · Retrieved July 2026 |
| License | CC BY 4.0 |

## Rankings

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | EzBioCloud: a genome-driven database and platform for microbiome identification and discovery | Mauricio Chalita, Yeong Ouk Kim, Sein Park, Hyun-Seok Oh, Jae Hyoung Cho, Jeongsup Moon, Nuga Baek, Changsik Moon, Kihyun Lee, Junwon Yang, Gi Gyun Nam, Yeonjae Jung, Seong-In Na, Michael James Bailey, Jongsik Chun | Mauricio Chalita | CJ Bioscience Inc, South Korea | INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | 203 | 10.1099/ijsem.0.006421 |
| 2 | The nature of the last universal common ancestor and its impact on the early Earth system | Edmund R R Moody, Sandra Álvarez-Carretero, Tara A Mahendrarajah, James W Clark, Holly C Betts, Nina Dombrowski, Lénárd L Szánthó, Richard A Boyle, Stuart Daines, Xi Chen, Nick Lane, Ziheng Yang, Graham A Shields, Gergely J Szöllősi, Anja Spang, Davide Pisani, Tom A Williams, Timothy M Lenton, Philip C J Donoghue | Edmund R. R. Moody, Davide Pisani, Tom A. Williams, Timothy M. Lenton, Philip C. J. Donoghue | University of Bristol, United Kingdom | Nature Ecology & Evolution | 169 | 10.1038/s41559-024-02461-1 |
| 3 | Soil microbiomes show consistent and predictable responses to extreme events | Christopher G Knight, Océane Nicolitch, Rob I Griffiths, Tim Goodall, Briony Jones, Carolin Weser, Holly Langridge, John Davison, Ariane Dellavalle, Nico Eisenhauer, Konstantin B Gongalsky, Andrew Hector, Emma Jardine, Paul Kardol, Fernando T Maestre, Martin Schädler, Marina Semchenko, Carly Stevens, Maria Α Tsiafouli, Oddur Vilhelmsson, Wolfgang Wanek, Franciska T de Vries | Christopher G. Knight, Robert I. Griffiths, Franciska T. de Vries | University of Manchester, United Kingdom | Nature | 138 | 10.1038/s41586-024-08185-3 |
| 4 | Nitrogen-fixing organelle in a marine alga | Tyler H Coale, Valentina Loconte, Kendra A Turk-Kubo, Bieke Vanslembrouck, Wing Kwan Esther Mak, Shunyan Cheung, Axel Ekman, Jian-Hua Chen, Kyoko Hagino, Yoshihito Takano, Tomohiro Nishimura, Masao Adachi, Mark Le Gros, Carolyn Larabell, Jonathan P Zehr | Tyler H. Coale, Valentina Loconte, Jonathan P. Zehr | University of California, Santa Cruz, United States | Science | 137 | 10.1126/science.adk1075 |
| 5 | The microbial carbon pump and climate change | Nianzhi Jiao, Tingwei Luo, Quanrui Chen, Zhao Zhao, Xilin Xiao, Jihua Liu, Zhimin Jian, Shucheng Xie, Helmuth Thomas, Gerhard J Herndl, Ronald Benner, Micheal Gonsior, Feng Chen, Wei-Jun Cai, Carol Robinson | Nianzhi Jiao | Xiamen University, China | Nature Reviews Microbiology | 136 | 10.1038/s41579-024-01018-0 |
| 6 | Global marine microbial diversity and its potential in bioprospecting | Jianwei Chen, Yangyang Jia, Ying Sun, Kun Liu, Changhao Zhou, Chuan Liu, Denghui Li, Guilin Liu, Chengsong Zhang, Tao Yang, Lei Huang, Yunyun Zhuang, Dazhi Wang, Dayou Xu, Qiaoling Zhong, Yang Guo, Anduo Li, Inge Seim, Ling Jiang, Lushan Wang, Simon Ming Yuen Lee, Yujing Liu, Dantong Wang, Guoqiang Zhang, Shanshan Liu, Xiaofeng Wei, Zhen Yue, Shanmin Zheng, Xuechun Shen, Sen Wang, Chen Qi, Jing Chen, Chen Ye, Fang Zhao, Jun Wang, Jie Fan, Baitao Li, Jiahui Sun, Xiaodong Jia, Zhangyong Xia, He Zhang, Junnian Liu, Yue Zheng, Xin Liu, Jian Wang, Huanming Yang, Karsten Kristiansen, Xun Xu, Thomas Mock, Shengying Li, Wenwei Zhang, Guangyi Fan | Ying Sun, Thomas Möck, Shengying Li, Wenwei Zhang, Guangyi Fan | BGI Research, China | Nature | 128 | 10.1038/s41586-024-07891-2 |
| 7 | Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally | Ziheng Peng, Xun Qian, Yu Liu, Xiaomeng Li, Hang Gao, Yining An, Jiejun Qi, Lan Jiang, Yiran Zhang, Shi Chen, Haibo Pan, Beibei Chen, Chunling Liang, Marcel G A van der Heijden, Gehong Wei, Shuo Jiao | Gehong Wei, Shuo Jiao | Northwest A&F University, China | Nature Communications | 107 | 10.1038/s41467-024-47348-8 |
| 8 | Reducing the uncertainty in estimating soil microbial-derived carbon storage | Han Hu, Chao Qian, Ke Xue, Rainer Georg Jörgensen, Marco Keiluweit, Chao Liang, Xuefeng Zhu, Ji Chen, Yishen Sun, Haowei Ni, Jixian Ding, Weigen Huang, Jingdong Mao, Rong-Xi Tan, Jizhong Zhou, Thomas W Crowther, Zhi-Hua Zhou, Jiabao Zhang, Yuting Liang | Hu Han, Chao Qian, Ke Xue, Chao Liang, Yuting Liang | Chinese Academy of Sciences, China | Proceedings of the National Academy of Sciences | 101 | 10.1073/pnas.2401916121 |
| 9 | Environmental stress mediates groundwater microbial community assembly | Daliang Ning, Yajiao Wang, Yupeng Fan, Jianjun Wang, Joy D Van Nostrand, Liyou Wu, Ping Zhang, Daniel J Curtis, Renmao Tian, Lauren Lui, Terry C Hazen, Eric J Alm, Matthew W Fields, Farris Poole, Michael W W Adams, Romy Chakraborty, David A Stahl, Paul D Adams, Adam P Arkin, Zhili He, Jizhong Zhou | Jizhong Zhou | University of Oklahoma, United States | Nature Microbiology | 95 | 10.1038/s41564-023-01573-x |
| 10 | Global analysis of soil bacterial genera and diversity in response to pH | Xuan Zhou, Teemu Tahvanainen, Lucie Malard, Liang Chen, Juliana Pérez-Pérez, Frank Berninger | Xuan Zhou | University of Eastern Finland, Finland | Soil Biology and Biochemistry | 94 | 10.1016/j.soilbio.2024.109552 |
| 11 | Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome | Niccolò Carlino, Aitor Blanco-Míguez, Michal Punčochář, Claudia Mengoni, Federica Pinto, Alessia Tatti, Paolo Manghi, Federica Armanini, Michele Avagliano, Coral Barcenilla, Samuel Breselge, Raul Cabrera-Rubio, Inés Calvete-Torre, Mairéad Coakley, José F Cobo-Díaz, Francesca De Filippis, Hrituraj Dey, John Leech, Eline S Klaassens, Stephen Knobloch, Dominic O'Neil, Narciso M Quijada, Carlos Sabater, Sigurlaug Skírnisdóttir, Vincenzo Valentino, Liam Walsh, MASTER EU Consortium, Avelino Alvarez-Ordóñez, Francesco Asnicar, Gloria Fackelmann, Vitor Heidrich, Abelardo Margolles, Viggó Thór Marteinsson, Omar Rota Stabelli, Martin Wagner, Danilo Ercolini, Paul D Cotter, Nicola Segata, Edoardo Pasolli | Niccolò Carlino | University of Trento, Italy | Cell | 93 | 10.1016/j.cell.2024.07.039 |
| 12 | Microbial trait multifunctionality drives soil organic matter formation potential | Emily D Whalen, A Stuart Grandy, Kevin M Geyer, Eric W Morrison, Serita D Frey | Emily D. Whalen | University of New Hampshire, United States | Nature Communications | 92 | 10.1038/s41467-024-53947-2 |
| 13 | Water periods impact the structure and metabolic potential of the nitrogen-cycling microbial communities in rivers of arid and semi-arid regions | Qingqing Pang, Guohua Zhao, Dan Wang, Xiang Zhu, Lei Xie, Dezhi Zuo, Longmian Wang, Linfeng Tian, Fuquan Peng, Bin Xu, Fei He, Jing Ding, Wenhai Chu | Dan Wang, Longmian Wang, Wenhai Chu | Nanjing Institute of Environmental Sciences, China | Water Research | 92 | 10.1016/j.watres.2024.122472 |
| 14 | Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming | Jing Tian, Jennifer A J Dungait, Ruixing Hou, Ye Deng, Iain P Hartley, Yunfeng Yang, Yakov Kuzyakov, Fusuo Zhang, M Francesca Cotrufo, Jizhong Zhou | Jing Tian, Fusuo Zhang, M. Francesca Cotrufo, Jizhong Zhou | China Agricultural University, China | Nature Communications | 84 | 10.1038/s41467-023-44647-4 |
| 15 | Biochar and organic fertilizer applications enhance soil functional microbial abundance and agroecosystem multifunctionality | Wang Hu, Yuping Zhang, Xiangmin Rong, Xuan Zhou, Jiangchi Fei, Jianwei Peng, Gongwen Luo | Yuping Zhang, Xuan Zhou, Gongwen Luo | Hunan Agricultural University, China | Biochar | 83 | 10.1007/s42773-023-00296-w |
| 16 | Simplified microbial network reduced microbial structure stability and soil functionality in alpine grassland along a natural aridity gradient | Chao Zhang, Shilong Lei, Hongyue Wu, Lirong Liao, Xiangtao Wang, Lu Zhang, Guobin Liu, Guoliang Wang, Linchuan Fang, Zilin Song | Zilin Song | Chinese Academy of Science, China | Soil Biology and Biochemistry | 81 | 10.1016/j.soilbio.2024.109366 |
| 17 | Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes | Nameer R Baker, Kateryna Zhalnina, Mengting Yuan, Don Herman, Javier A Ceja-Navarro, Joelle Sasse, Jacob S Jordan, Benjamin P Bowen, Liyou Wu, Christina Fossum, Aaron Chew, Ying Fu, Malay Saha, Jizhong Zhou, Jennifer Pett-Ridge, Trent R Northen, Mary K Firestone | Nameer Baker, Kateryna Zhalnina, Mary K. Firestone | University of California, Berkeley, United States | Proceedings of the National Academy of Sciences | 80 | 10.1073/pnas.2303439121 |
| 18 | Achieving Stable Partial Denitrification by Selective Inhibition of Nitrite Reductase with the Biosafe Aprotic Solvent DMSO | Zhi-Bin Wang, Jinpeng Zhang, Qinshu Miao, Hai-Yan Cao, Fei Xiong, Taeho Lee, Amro El-Baz, Liangke Xie, Shou-Qing Ni | Shou‐Qing Ni | Shandong University, China | Environmental Science & Technology | 80 | 10.1021/acs.est.4c08731 |
| 19 | Unlocking bacterial potential to reduce farmland N2O emissions | Elisabeth G Hiis, Silas H W Vick, Lars Molstad, Kristine Røsdal, Kjell Rune Jonassen, Wilfried Winiwarter, Lars R Bakken | Lars R. Bakken | Norwegian University of Life Sciences, Norway | Nature | 79 | 10.1038/s41586-024-07464-3 |
| 20 | Insights into plant interactions and the biogeochemical role of the globally widespread Acidobacteriota phylum | Osiel Silva Gonçalves, Alexia Suellen Fernandes, Sumaya Martins Tupy, Tauanne G. Ferreira, Luciano N. Almeida, Christopher J. Creevey, Mateus Ferreira Santana | Mateus Ferreira Santana | Universidade Federal de Viçosa, Brazil | Soil Biology and Biochemistry | 78 | 10.1016/j.soilbio.2024.109369 |

## Topic trends

### What Topics Define the Class of 2026?

The Class of 2026 is defined by a deep focus on microbial physiology in environmental contexts, with "Microbial carbon use efficiency" emerging as the most prominent informative concept. This highlights a shift from simply describing who is there to understanding how microbes process carbon and energy. Foundational profiling techniques—specifically "16S rRNA gene sequencing" and "Metagenomics"—remain central to the field, providing the necessary resolution to map community structures. Additionally, "Microbial necromass" and "Soil microbiome" feature heavily, indicating strong continued interest in carbon sequestration and soil health dynamics. Together, these themes reflect an ecology field increasingly focused on the mechanistic links between community composition and biogeochemical outcomes.

*Leading research themes*

### How Did Topics Shift from the Class of 2025 to the Class of 2026?

The transition to the Class of 2026 reveals a distinct pivot toward stress responses and complex interaction modeling. "Salt stress" and "Microbial network complexity" experienced dramatic surges, rising from negligible frequencies in the previous cohort to become major themes in 2026. This indicates a rapidly growing interest in how microbial networks adapt to environmental extremes. "Microbial carbon use efficiency" also saw a substantial increase, reinforcing its dominance as a core metabolic metric. Conversely, broader community descriptors like "Bacterial community" and "Community assembly" declined, suggesting that researchers are moving beyond general community characterization toward targeted investigations of specific stressors and intricate network dynamics.

*How topics shifted year over year*

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Microbial Community Ecology and Physiology Papers, Class of 2026. https://pri.pepkio.com/top-papers/microbial-community-ecology-and-physiology/2026. Accessed 2026-07-21.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459
```