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Microorganisms
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Soil Microbial Communities and Ecosystem Functions
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Soil Microbial Communities and Ecosystem Functions

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 9966

Special Issue Editor

Prof. Dr. Efimia M. Papatheodorou

E-Mail Website
Guest Editor
Department of Ecology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
Interests: soil microbial community structure and function; enzymes in soil; soil restoration; soil quality and agricultural practices
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil microbial communities play essential roles in maintaining ecosystem functions such as litter decomposition, mineralization, nitrification and denitrification, exerting control on primary production, soil fertility and the emission of gasses. Disturbances inducing changes in habitat connectivity, nutrient inputs and global environmental variables due to changes in land use and climate affect the composition and structure of soil microbial communities, with subsequent changes in ecosystem functions. However, the relation between the community assemblage and a specific function or an index of multifunctionality could be affected by a variety of factors. These are variables used to assess community organization (functional diversity, species richness, composition, co-occurrence patterns), those referred to the taxonomic level of the community organisation as well as variables that are related to the spatial scale of community (local, global or in the cross-boundary areas). Most studies have explored the relation between species/taxa richness and functions, and there is a gap concerning the relationship between the co-occurrence patterns of microbes and the functionality of an ecosystem. Furthermore, information concerning the influence of the spatial scale of analysis or the temporal pattern of the environmental changes (constant or with oscillations) is very rare. Knowledge of the relation between soil microbes and soil functionality could be extremely useful for conservation, restoration and management efforts.

In this Special Issue of Microorganisms, we invite authors to send their contributions concerning any aspect that could affect the relationships between microbial organization and soil functionality: metrics of analysis, spatial scale or different environmental conditions, as well as the influence of perturbations on the above-mentioned relationships. In this Special Issue we welcome original research papers, review articles, and short communications. Research areas may include, but are not limited to, ecology, microbiology, and biogeography.

I look forward to receiving your contributions. 

Prof. Dr. Efimia M. Papatheodorou
Guest Editor

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

  • soil functionality
  • functional diversity
  • soil microbial communities
  • disturbances
  • co-occurrence patterns
  • environmental oscillations
  • microbial assemblages

Published Papers (6 papers)

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Editorial

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4 pages, 483 KiB  
Editorial
Interventions Change Soil Functions and the Mechanisms Controlling the Structure of Soil Microbial Communities
by Effimia M. Papatheodorou
Microorganisms 2023, 11(6), 1502; https://doi.org/10.3390/microorganisms11061502 - 05 Jun 2023
Viewed by 952
Abstract
Soil microbial communities play essential roles in maintaining ecosystem functions, such as litter decomposition, mineralization, nitrification, and denitrification, thus exerting control on primary production, soil fertility, and gas emissions [...] Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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Research

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14 pages, 2340 KiB  
Article
Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns
by Effimia M. Papatheodorou, Spiros Papakostas and George P. Stamou
Microorganisms 2023, 11(3), 790; https://doi.org/10.3390/microorganisms11030790 - 19 Mar 2023
Cited by 2 | Viewed by 1255
Abstract
Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present [...] Read more.
Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU. Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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14 pages, 1851 KiB  
Article
Responses of Rhizosphere Bacterial and Fungal Communities to the Long-Term Continuous Monoculture of Water Oat
by Gang Wu, Feifei Yu, Manman Yuan, Jiabao Wang, Chuang Liu, Weizhu He, Zhihuan Ge, Yixiang Sun and Yuan Liu
Microorganisms 2022, 10(11), 2174; https://doi.org/10.3390/microorganisms10112174 - 02 Nov 2022
Cited by 7 | Viewed by 1481
Abstract
As an cultivated aquatic vegetable, the long-term continuous monocropping of water oat results in the frequent occurrence of diseases, the deterioration of ecological system and decreased quality of water oat. In this study, real-time quantitative PCR (qPCR) and Illumina high-throughput sequencing were used [...] Read more.
As an cultivated aquatic vegetable, the long-term continuous monocropping of water oat results in the frequent occurrence of diseases, the deterioration of ecological system and decreased quality of water oat. In this study, real-time quantitative PCR (qPCR) and Illumina high-throughput sequencing were used to determine the dynamic changes in bacterial and fungal communities in rhizosphere soil under continuous cropping of water oat for 1, 5, 10, 15 and 20 years (Y1, Y5, Y10, Y15 and Y20), and soil properties and enzyme activities were also determined. Results showed that the contents of soil organic carbon (SOC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP) and the activities of four soil enzymes increased in Y5 and Y10 and then decreased in Y15 and Y20. Spearman correlation analysis identified SOC, TN, AP and AN as the main factors that affect the four enzyme activities. The qPCR results showed that there was no significant difference in bacterial abundance between the different planting years, while the fungal abundance first increased and then decreased. The long-term continuous planting of water oat (Y15 and Y20) significantly reduced the operational taxonomic unit numbers and the Shannon, Chao1, and ACE indices of rhizosphere bacteria and fungi. The bacterial and fungal community compositions were markedly affected by the continuous planting year. The relative abundances of Bacteroidetes and Firmicutes decreased significantly in Y10 and Bacteroidetes increased significantly in Y15. Relative abundances of dominated Mortierellomycota and Ascomycota phyla increased with the continuous cropping years, while Rozellomycota presented the opposite trend. The AK, AN, and SOC were the main factors that changed the bacterial community, while AK and AP significantly shifted the fungal community. Thus, long-term continuous planting of water oat resulted in the deterioration of soil nutrients and microbial communities. The results provided a reference for the remediation of soil under continuous water oat planting and sustainable development of water oat industry. Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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13 pages, 1915 KiB  
Article
Legacy Effects of Biochar and Compost Addition on Arbuscular Mycorrhizal Fungal Community and Co-Occurrence Network in Black Soil
by Ying Xin, Yi Fan, Olubukola Oluranti Babalola, Ximei Zhang and Wei Yang
Microorganisms 2022, 10(11), 2137; https://doi.org/10.3390/microorganisms10112137 - 28 Oct 2022
Cited by 5 | Viewed by 1649
Abstract
Compost and biochar are beneficial soil amendments which derived from agricultural waste, and their application was proven to be effective practices for promoting soil fertility. Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species, and are recognized as one group [...] Read more.
Compost and biochar are beneficial soil amendments which derived from agricultural waste, and their application was proven to be effective practices for promoting soil fertility. Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species, and are recognized as one group of the most important soil microorganisms to increase food security in sustainable agriculture. To understand the legacy effects of compost and biochar addition on AM fungal communities, a field study was conducted on the Songnen Plain, Northeast China. Two years after application, compost addition improved soil aggregate stability, but we did not detect a legacy effect of compost addition on AM fungal community. Our results indicated that AM fungal Shannon diversity and Pielou evenness indices were significantly increased by one-time biochar addition, but unaffected by compost addition after two year’s application. PERMANOVA analysis also revealed a legacy effect of biochar addition on AM fungal community. Network analysis revealed a dramatically simplified AM fungal co-occurrence network and small network size in biochar added soils, demonstrated by their topological properties (e.g., low connectedness and betweenness). However, AM fungal community did not differ among aggregate fractions, as confirmed by the PERMANOVA analysis as well as the fact that only a small number of AM fungal OTUs were shared among aggregate fractions. Consequently, the current study highlights a stronger legacy effect of biochar than compost addition on AM fungi, and have implications for agricultural practices. Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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13 pages, 3309 KiB  
Article
Tillage Promotes the Migration and Coexistence of Bacteria Communities from an Agro-Pastoral Ecotone of Tibet
by Yuhong Zhao, Mingtao Wang, Yuyi Yang, Peng Shang and Weihong Zhang
Microorganisms 2022, 10(6), 1206; https://doi.org/10.3390/microorganisms10061206 - 13 Jun 2022
Cited by 1 | Viewed by 1520
Abstract
In the Tibetan agro-pastoral ecotone, which has an altitude of 4000 m above sea level, small-scale cropland tillage has been exploited on the grassland surrounding the houses of farmers and herdsmen. However, knowledge of the effects of land change from grassland to cropland [...] Read more.
In the Tibetan agro-pastoral ecotone, which has an altitude of 4000 m above sea level, small-scale cropland tillage has been exploited on the grassland surrounding the houses of farmers and herdsmen. However, knowledge of the effects of land change from grassland to cropland on soil nutrients and microbial communities is poor. Here, we investigated the structure and assembly mechanism of bacterial communities in cropland (tillage) and grassland (non-tillage) from an agro-pastoral ecotone of Tibet. Results indicated that soil nutrients and composition of bacterial communities changed dramatically in the process of land-use change from grassland to cropland. The pH value and the content of total nitrogen, organic material, total potassium, and total phosphorus in cropland soil were well above those in grassland soil, whereas the soil bulk density and ammonia nitrogen content in grassland soil were higher than those in cropland soil. Proteobacteria (30.5%) and Acidobacteria (21.7%) were the key components in cropland soil, whereas Proteobacteria (31.5%) and Actinobacteria (27.7%) were the main components in grassland soils. Tillage promotes uniformity of bacterial communities in cropland soils. In particular, the higher migration rate may increase the coexistence patterns of the bacterial community in cropland soils. These results also suggest that the tillage promotes the migration and coexistence of bacterial communities in the grassland soil of an agro-pastoral ecotone. In addition, the stochastic process was the dominant assembly pattern of the bacterial community in cropland, whereas, in grassland soil, the community assembly was more deterministic. These findings provide new insights into the changes in soil nutrients and microbial communities during the conversion of grassland to cropland in the agro-pastoral ecotone. Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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Other

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8 pages, 262 KiB  
Perspective
Current Challenges and Pitfalls in Soil Metagenomics
by Marcio F. A. Leite, Sarah W. E. B. van den Broek and Eiko E. Kuramae
Microorganisms 2022, 10(10), 1900; https://doi.org/10.3390/microorganisms10101900 - 25 Sep 2022
Cited by 6 | Viewed by 2245
Abstract
Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated [...] Read more.
Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility. Full article
(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)
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