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Biology
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Recent Advances in Soil Health: Influences of Organic Carbon and...
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Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 18477

Special Issue Editors

Dr. Audrius Kačergius

E-Mail Website
Guest Editor
Voke Branch, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Žalioji a. 2, LT 02232 Vilnius, Lithuania
Interests: soil properties and microbiology; plants pathology; molecular biology; biomass conversion process
Special Issues, Collections and Topics in MDPI journals
Dr. Audrius Gegeckas

E-Mail Website
Guest Editor
Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis av. 7, LT-10257 Vilnius, Lithuania
Interests: soil health; soil microbiota; biofertilizers; plant growth-promoting bacteria; biocatalysis
Dr. Renata Gudiukaité

E-Mail Website
Guest Editor
Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis av. 7, LT-10257 Vilnius, Lithuania
Interests: engineering of microbial enzymes; bioconsolidation/biocementation; polyester hydrolysis; biocontrol of micromycetes; soil improvement

Special Issue Information

Dear Colleagues,

Recently, the deteriorating general condition of the soil has become a cause of great concern. Much scientific research has been directed to searching for measures that can improve the ability of soil to accumulate organic carbon, thus preventing degradation and improving the availability of nutrients to plants. The state of soil organic matter is the main quality parameter of the soil. Environmental factors (temperature, oxygen availability, humidity, biological activity) determine the quality and speed of decomposition of organic matter, which is very important in intensive agricultural systems. However, the assessment of soil health is still dominated by chemical indicators, although there are enough signals to demonstrate the importance of soil biodiversity. The understanding of soil health should be enriched by the ability to absorb carbon, in the form of CO2, thereby contributing to climate change mitigation, and the accumulation of soil carbon stocks, ensuring the long-term sustainability of ecosystems and the maintenance of productivity. In this case, not only are the quantitative parameters of the soil microbiota very important, but also the composition of species, as well as the functional capabilities that determine the success of nutrients entering the soil and the general condition of the soil and, most importantly, its sustainability. Currently, the use of beneficial microorganisms in the agricultural sector is increasing, in order to replace mineral fertilizers and chemical pesticides. The control of soil health should be considered as a fundamental principle in achieving sustainability as an ultimate goal.

Therefore, we invite scientists to publish their latest research results in the field of soil health in scientific articles and reports, and to share their insights on this topic in review articles. Scientific articles concerning the research on the diversity of soil microorganism communities, including viruses, protozoa, and invertebrates, in the sense of analyzing the condition of the soil health are also very welcome.

Dr. Audrius Kačergius
Dr. Audrius Gegeckas
Dr. Renata Gudiukaité
Guest Editors

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. Biology 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

  • diversity of soil microbial community
  • soil microbial function in environment
  • soil microbiomics
  • carbon sequestration
  • soil organic matter (SOM)
  • soil organic carbon (SOC)
  • soil quality
  • plant–soil microbial interaction
  • eco-friendly agriculture
  • biofertilizers

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Published Papers (6 papers)

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Editorial

Jump to: Research, Review

3 pages, 161 KiB  
Editorial
Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota
by Audrius Kačergius, Audrius Gegeckas and Renata Gudiukaitė
Biology 2025, 14(5), 500; https://doi.org/10.3390/biology14050500 - 4 May 2025
Viewed by 222
Abstract
As the deterioration of the overall condition of soils is a growing concern, more and more attention is being paid in the scientific literature to the search for and analysis of measures that can improve the ability of the soil to accumulate organic [...] Read more.
As the deterioration of the overall condition of soils is a growing concern, more and more attention is being paid in the scientific literature to the search for and analysis of measures that can improve the ability of the soil to accumulate organic carbon and increase the availability of nutrients to plants [...] Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)

Research

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23 pages, 10673 KiB  
Article
Improvement Effects of Different Afforestation Measures on the Surface Soil of Alpine Sandy Land
by Shaobo Du, Huichun Xie, Gaosen Zhang, Feng Qiao, Guigong Geng and Chongyi E
Biology 2025, 14(2), 144; https://doi.org/10.3390/biology14020144 - 30 Jan 2025
Cited by 1 | Viewed by 754
Abstract
Desertification severely impacts soil environments, necessitating effective control measures to improve sandy soil. On the alpine sandy land of Gonghe Basin, taking bare land containing mobile sand dunes (LD) as a reference, surface soil undergoing four afforestation measures, namely Salix cheilophila + [...] Read more.
Desertification severely impacts soil environments, necessitating effective control measures to improve sandy soil. On the alpine sandy land of Gonghe Basin, taking bare land containing mobile sand dunes (LD) as a reference, surface soil undergoing four afforestation measures, namely Salix cheilophila + Populus simonii (WLYY), Salix psammophila + Salix cheilophila (SLWL), Artemisia ordosica + Caragana korshinskii (SHNT), and Caragana korshinskii (NT80), was studied, with soil physicochemical properties and enzyme activity measured and the bacterial community structure analyzed using Illumina high-throughput sequencing. Compared to LD, all four afforestation measures significantly reduced the sand content, while increasing soil total carbon, total nitrogen, organic matter, alkali-hydrolyzable nitrogen, and available potassium. WLYY, SLWL, and SHNT significantly increased the surface soil total phosphorus and total potassium. Catalase, sucrase, urease, and alkaline phosphatase activities significantly increased under all four measures. Among them, the highest improvements were observed under SLWL, followed by WLYY. All treatments increased soil bacterial community richness, exhibiting significantly different bacterial community compositions to those in LD. Total phosphorus was the key physicochemical factor affecting the soil bacterial community structure, while enzyme activity was significantly correlated with the relative abundance of most major bacterial phyla. All measures improved the surface soil environment, with SLWL demonstrating the best improvement. The results provide valuable reference for sand prevention and control strategies in alpine sandy areas and offer a theoretical basis for the ecological restoration of sandy soil microenvironments. Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)
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21 pages, 5230 KiB  
Article
Soil Microbial Community Structure and Carbon Stocks Following Fertilization with Organic Fertilizers and Biological Inputs
by Diana Sivojienė, Aistė Masevičienė, Lina Žičkienė, Almantas Ražukas and Audrius Kačergius
Biology 2024, 13(7), 534; https://doi.org/10.3390/biology13070534 - 17 Jul 2024
Cited by 3 | Viewed by 1510
Abstract
The application of organic fertilizers and biological inputs to soil inevitably affects its quality, agrochemical indicators, and microbiota. Sustainable agriculture is based on continuously learning about how to properly manage available soil, water, and biological resources. The aim of the study was to [...] Read more.
The application of organic fertilizers and biological inputs to soil inevitably affects its quality, agrochemical indicators, and microbiota. Sustainable agriculture is based on continuously learning about how to properly manage available soil, water, and biological resources. The aim of the study was to determine changes in microorganism communities and carbon stocks in infertile soils for fertilization using different organic fertilizers and their combinations with bio-inputs. Genetic analysis of microorganism populations was performed using the NGS approach. Our study showed that the application of organic fertilizers affects the soil microbiota and the taxonomic structure of its communities. Specific groups of bacteria, such as Bacillota, were promoted by organic fertilization, meanwhile the abundance of Pseudomonadota and Ascomycota decreased in most treatments after the application of poultry manure. Metagenomic analysis confirmed that the use of bio-inputs increased the relative abundance of Trichoderma spp. fungi; meanwhile, a significant change was not found in the representatives of Azotobacter compared to the treatments where the bio-inputs were not used. The positive influence of fertilization appeared on all the studied agrochemical indicators. Higher concentrations of Corg and Nmin accumulated in the soil when we used granulated poultry manure, and pHKCl when we used cattle manure. Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)
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16 pages, 1478 KiB  
Article
Ecological Diversity of Bacterial Rhizomicrobiome Core during the Growth of Selected Wheat Cultivars
by Agnieszka Kuźniar, Kinga Włodarczyk, Sara Jurczyk, Ryszard Maciejewski and Agnieszka Wolińska
Biology 2023, 12(8), 1067; https://doi.org/10.3390/biology12081067 - 30 Jul 2023
Cited by 2 | Viewed by 2035
Abstract
One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of [...] Read more.
One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of wheat rhizosphere communities with wheat (W) and legume (L) forecrops determined by three different methods in this study (membership, composition, and functionality). The conclusions of the three methods of microbiome core definition suggest the presence of generalists, i.e., some representative microorganisms from Proteobacteria, Actinobacteria, Hypomicrobiaceae, Bradyrhizobiaceae, Sphingomonas sp., in the wheat rhizomicrobiome. The relative abundance of the core microbiome accounted for 0.1976% (W) and 0.334% (L)—membership method and 6.425% (W) and 4.253% (L)—composition method. Additionally, bacteria of the specialist group, such as Rhodoplanes sp., are functionally important in the rhizomicrobiome core. This small community is strongly connected with other microbes and is essential for maintenance of the sustainability of certain metabolic pathways. Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)
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Review

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14 pages, 646 KiB  
Review
Soil Microbial Carbon Use Efficiency in Natural Terrestrial Ecosystems
by Weirui Yu, Lianxi Sheng, Xue Wang, Xinyu Tang, Jihong Yuan and Wenbo Luo
Biology 2025, 14(4), 348; https://doi.org/10.3390/biology14040348 - 27 Mar 2025
Cited by 1 | Viewed by 535
Abstract
Soil microbial carbon use efficiency (CUE) is the ratio of carbon allocated to microbial growth to that taken up by microorganisms. Soil microbial CUE affects terrestrial ecosystem processes such as greenhouse gas emissions, carbon turnover, and sequestration, which is an important indicator of [...] Read more.
Soil microbial carbon use efficiency (CUE) is the ratio of carbon allocated to microbial growth to that taken up by microorganisms. Soil microbial CUE affects terrestrial ecosystem processes such as greenhouse gas emissions, carbon turnover, and sequestration, which is an important indicator of changes in the terrestrial carbon cycle. Firstly, we summarized the three methods of soil microbial CUE, stoichiometric modeling, 13C glucose tracing, and 18O water tracing, and compared the advantages and limitations of the three methods. Then, we analyzed the single or combined effects of different environmental factors on soil microbial CUE in grassland ecosystems, forest ecosystems, and wetland ecosystems. Finally, we suggested that future research should focus on the following aspects: the influence of management patterns on CUE (such as grazing and the prohibition of grazing in grassland ecosystems, forest gap, and thinning in forest ecosystems); effects of the strategies of microorganisms for adapting to environmental changes on CUE; effects of anaerobic metabolic pathways, especially in wetland ecosystems; and effects of microbial taxonomic level. This study contributes to the investigation of the microbial mechanisms of carbon cycling in terrestrial ecosystems to mitigate the impacts of climate change. Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)
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39 pages, 1383 KiB  
Review
Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem
by Jokūbas Daunoras, Audrius Kačergius and Renata Gudiukaitė
Biology 2024, 13(2), 85; https://doi.org/10.3390/biology13020085 - 29 Jan 2024
Cited by 78 | Viewed by 12385
Abstract
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing [...] Read more.
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions. Full article
(This article belongs to the Special Issue Recent Advances in Soil Health: Influences of Organic Carbon and Microbiota)
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