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Journals
Microorganisms
Special Issues
Microbial Communities and Nitrogen Cycling
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Microbial Communities and Nitrogen Cycling

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 2422

Special Issue Editors

Prof. Dr. Chen Ye

E-Mail Website
Guest Editor
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: microbial communities; nitrogen cycle; environmental changes; microbial diversity; biogeochemical processes; nitrogen fixation; nitrification; denitrification; ecosystem health
Dr. Yu Gong

E-Mail Website
Guest Editor Assistant
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: climate change; greenhouse gas; carbon cycling; wetland; air pollution
Special Issues, Collections and Topics in MDPI journals
Dr. Hao Liao

E-Mail
Guest Editor Assistant
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: soil microbiology; carbon cycle; soil aggregates

Special Issue Information

Dear Colleagues,

The nitrogen cycle is a fundamental biogeochemical process that underpins life on Earth, involving the transformation of nitrogen between its various chemical forms. Microbial communities play a pivotal role in this cycle, mediating processes such as nitrogen fixation, nitrification, denitrification, and ammonification. This Special Issue aims to explore the intricate relationships between microbial communities and nitrogen cycling, highlighting recent research findings, technological advancements, and theoretical insights. We welcome submissions that examine the diversity, function, and resilience of microbial populations in various ecosystems, as well as studies that investigate the impact of environmental changes on nitrogen cycling processes. By bringing together interdisciplinary research, this issue seeks to foster a deeper understanding of the complex dynamics within microbial nitrogen transformations and their implications for ecosystem health and global biogeochemical cycles.

Prof. Dr. Chen Ye
Guest Editor

Dr. Yu Gong
Dr. Hao Liao
Guest Editor Assistants

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial communities
  • nitrogen cycle
  • biogeochemical processes
  • nitrogen fixation
  • nitrification
  • denitrification
  • ammonification
  • ecosystem health
  • environmental changes
  • microbial diversity

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Published Papers (3 papers)

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Research

23 pages, 9041 KiB  
Article
Microbial Community Responses and Nitrogen Cycling in the Nitrogen-Polluted Urban Shi River Revealed by Metagenomics
by Ran Wang, Shang Yang and Wei Zhao
Microorganisms 2025, 13(5), 1007; https://doi.org/10.3390/microorganisms13051007 - 27 Apr 2025
Viewed by 224
Abstract
Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021–2023) water quality monitoring with metagenomic sequencing to investigate [...] Read more.
Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021–2023) water quality monitoring with metagenomic sequencing to investigate microbial community dynamics, nitrogen cycling processes, and their responses to nitrogen pollution in the Shi River, Qinhuangdao, China. Nitrogen pollution was predominantly derived from industrial discharges from enterprises in the Shi River Reservoir upstream (e.g., coolant and chemical effluents), agricultural runoff, untreated domestic sewage (particularly from catering and waste in Pantao Valley), and livestock farming effluents. Total nitrogen (TN) concentrations ranged from 2.22 to 6.44 mg/L, exceeding China’s Class V water standard (2.0 mg/L, GB 3838-2002), with the highest level at the urbanized W4 site (6.44 mg/L). Nitrate nitrogen (NO3-N) accounted for 60–80% of TN. Metagenomic analysis revealed Fragilaria, Microcystis, and Flavobacterium thriving (up to 15% relative abundance) under nitrogen stress, with nitrogen metabolism genes (narG, nifH, nirK) enriched at polluted sites (W2, W4), narG reaching 26% at W1. Dissolved oxygen positively correlated with nitrate reductase gene abundance, while ammonia nitrogen inhibited it. Burkholderiales and Limnohabitans dominated denitrification, offering insights into sustainable urban river management. Full article
(This article belongs to the Special Issue Microbial Communities and Nitrogen Cycling)
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15 pages, 3707 KiB  
Article
Limited Effect of Biodiversity on the Multifunctionality of a Revegetated Riparian Ecosystem
by Yueliang Jiang, Chen Ye, Manuel Delgado-Baquerizo, Guiyao Zhou, Yu Gong and Quanfa Zhang
Microorganisms 2025, 13(3), 554; https://doi.org/10.3390/microorganisms13030554 - 28 Feb 2025
Cited by 1 | Viewed by 553
Abstract
Vegetation and microbial diversity play an essential role in ecosystem function. Active ecosystem restoration costs millions of dollars to increase biodiversity, yet when and how this restoration is effective when aiming at restoring multiple ecosystem functions (EMF) is still under debate. Here, we [...] Read more.
Vegetation and microbial diversity play an essential role in ecosystem function. Active ecosystem restoration costs millions of dollars to increase biodiversity, yet when and how this restoration is effective when aiming at restoring multiple ecosystem functions (EMF) is still under debate. Here, we investigated the influence of a decade of restoration practices (i.e., active revegetation vs. natural rewilding) on the recovery of the ecosystem multifunctionality (EMF) provided by a riparian ecosystem. The experiment was conducted within the region of China’s Three Gorges Dam, and the area was subjected to a gradient of flooding disturbance. We found that active revegetation increased the plant diversity by 13~57% and EMF by ~2.6 times at the extreme flooding zone (~286 flooding days/year) of the riparian ecosystem, when compared with natural rewilding. Moreover, the positive relationship between plant diversity and EMF was weak, and abiotic factors (soil aggregate, pH, soil water content, and heavy metal content) were the dominant predictors for EMF, explaining 52% of the EMF variation. Revegetation impacted EMF both directly and indirectly via altering the soil properties. In addition, we also observed important trade-offs between plant biomass and soil functions (carbon storage and fertility). This study provides critical insights into whether and how a decade of active restoration is effective to recover the EMF supported by riparian ecosystems, and it highlights the importance of active revegetation in conservation and management programs for riparian ecosystems under future extreme flooding conditions. Full article
(This article belongs to the Special Issue Microbial Communities and Nitrogen Cycling)
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20 pages, 3377 KiB  
Article
Response of Soil Bacteria to Short-Term Nitrogen Addition in Nutrient-Poor Areas
by Hongbin Yin, Mingyi Xu, Qingyang Huang, Lihong Xie, Fan Yang, Chao Zhang, Gang Sha and Hongjie Cao
Microorganisms 2025, 13(1), 56; https://doi.org/10.3390/microorganisms13010056 - 1 Jan 2025
Viewed by 868
Abstract
Increasing nitrogen (N) addition induces soil nutrient imbalances and is recognized as a major regulator of soil microbial communities. However, how soil bacterial abundance, diversity, and community composition respond to exogenous N addition in nutrient-poor and generally N-limited regions remains understudied. In this [...] Read more.
Increasing nitrogen (N) addition induces soil nutrient imbalances and is recognized as a major regulator of soil microbial communities. However, how soil bacterial abundance, diversity, and community composition respond to exogenous N addition in nutrient-poor and generally N-limited regions remains understudied. In this study, we investigated the effects of short-term exogenous N additions on soil bacterial communities using quantitative polymerase chain reaction (PCR) and Illumina Miseq sequencing in an in situ N addition field experiment. The results showed that a low nitrogen addition increased the observed species (Sobs) of the bacterial community, and with the increased nitrogen addition, the Sobs of bacteria gradually decreased, especially the unique OTUs. The relative abundance of Proteobacteria, Actinobacteria, and Gemmatimonadetes increased with increasing nitrogen addition, whereas the relative abundance of Chloroflexi and Firmicutes decreased. Soil properties play an important role in bacterial community structure at phylum or genus levels. Short-term nitrogen addition increased the proportion of nodes from Actinobacteria and Proteobacteria in the co-occurrence network and enhanced the stability of the microbial network. Actinobacteria may play an important role in constructing the network. Our study aims to explore the effects of nitrogen addition on the diversity, composition, and structure of soil bacterial communities in nutrient-poor areas caused by ecological disturbances. Full article
(This article belongs to the Special Issue Microbial Communities and Nitrogen Cycling)
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