Special Issue "Role of Soil Organisms in Modification of their Environment, Nutrient Cycling and Soil Formation"

A special issue of Soil Systems (ISSN 2571-8789).

Deadline for manuscript submissions: closed (28 February 2021).

Special Issue Editors

Prof. Dr. Jan Frouz
E-Mail Website
Guest Editor
Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, 128 44 Prague 2, Czech Republic
Interests: soil fauna; ecosystem restoration; ecosystem ecology
Special Issues and Collections in MDPI journals
Dr. Veronika Jílková
E-Mail Website
Guest Editor
Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology and SoWa RI, Na Sádkách 7, CZ-37005 České Budějovice, Czech Republic
Interests: organic matter decomposition; carbon sequestration; soil nutrient cycling; activity and abundance of soil fauna and microorganisms

Special Issue Information

Dear Colleagues,

Soil organisms play a principal role in modification of their environment, nutrient cycling and soil formation. These effects can be achieved by contribution of soil biota to food webs which facilitates mineralization of soil organic matter and release of nutrients. Many soil organisms contribute to processes of nutrient transformation for other means connected to energy metabolism. Beside these processes related to energy metabolism, Soil organisms contribute to formation of soil structure and build-up of soil aggregates which, when accumulated, may contribute to formation of soil layers and eventually alter conditions of the whole soil profile. An important feature of these functions of soil biota is the interaction of organisms which vary in size in several orders of magnitudes. This interaction among an extremely variable range of organisms varies in space and time and upscaling this interaction to large spatio-temporal scales often brings another layer of complexity. The subject of this special issue is to cover all the above mentioned aspects of nutrient cycling and soil structure formation and modification affected by soil biota. In particular, we are interested in understanding the mechanisms based on the interaction among soil organisms at various spatio-temporal scales.

Prof. Dr. Jan Frouz
Dr. Veronika Jílková
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 papers will be 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. Soil Systems is an international peer-reviewed open access quarterly 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 1400 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

  • microorganisms
  • fauna
  • organic matter
  • soil aggregates
  • soil structure

Published Papers (10 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

Article
Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons
Soil Syst. 2021, 5(1), 14; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems5010014 - 25 Feb 2021
Cited by 2 | Viewed by 826
Abstract
Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study [...] Read more.
Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research. Full article
Show Figures

Figure 1

Article
Zero Tillage Systems Conserve Arbuscular Mycorrhizal Fungi, Enhancing Soil Glomalin and Water Stable Aggregates with Implications for Soil Stability
Soil Syst. 2021, 5(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems5010004 - 13 Jan 2021
Cited by 2 | Viewed by 999
Abstract
Arbuscular Mycorrhizal (AM) fungi form mutualistic symbiotic relationships with approximately 80% of terrestrial plant species, while producing the glycoprotein glomalin as a structural support molecule along their mycelial network. Glomalin confers two benefits for soils: (1) acting as a carbon and nitrogen storage [...] Read more.
Arbuscular Mycorrhizal (AM) fungi form mutualistic symbiotic relationships with approximately 80% of terrestrial plant species, while producing the glycoprotein glomalin as a structural support molecule along their mycelial network. Glomalin confers two benefits for soils: (1) acting as a carbon and nitrogen storage molecule; (2) the binding of soil microaggregates (<250 µm) to form larger, more stable structures. The present study aimed to test the hypothesis that a correlation between glomalin and soil aggregation exists and that this is influenced by the method of seedbed preparation. The soils from two crops of winter wheat in Hertfordshire, UK, practising either conventional (20 cm soil inversion) or zero tillage exclusively, were sampled in a 50 m grid arrangement over a 12 month period. Glomalin and water stable aggregates (WSA) were quantified for each soil sample and found to be significantly greater in zero tillage soils compared to those of conventional tillage. A stronger correlation between WSA and glomalin was observed in zero tillage (Pearson’s coeffect 0.85) throughout the cropping year compared to conventional tillage (Pearson’s coeffect 0.07). The present study was able to conclude that zero tillage systems are beneficial for AM fungi, the enhancement of soil glomalin and soil erosion mitigation. Full article
Show Figures

Figure 1

Article
Correlations of Soil Fungi, Soil Structure and Tree Vigour on an Apple Orchard with Replant Soil
Soil Syst. 2020, 4(4), 70; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4040070 - 03 Dec 2020
Cited by 3 | Viewed by 1024
Abstract
The soil-borne apple replant disease (ARD) is caused by biotic agents and affected by abiotic properties. There is evidence for the interrelation of the soil fungal population and soil aggregate structure. The aim of this study conducted between March and October 2020 on [...] Read more.
The soil-borne apple replant disease (ARD) is caused by biotic agents and affected by abiotic properties. There is evidence for the interrelation of the soil fungal population and soil aggregate structure. The aim of this study conducted between March and October 2020 on an orchard in north-east Germany was to detect the correlations of soil fungal density, soil structure and tree vigour under replant conditions in a series of time intervals. By using the replant system as the subject matter of investigation, we found that replanting had an impact on the increase of soil fungal DNA, which correlated with a mass decrease of large macro-aggregates and an increase of small macro- and large micro-aggregates in the late summer. Increased proportions of water-stable aggregates (WS) with binding forces ≤ 50 J mL−1, decreased proportions of WS > 100 J mL−1 and a decrease of the mean weight diameter of aggregates (MWD) emphasised a reduction of aggregate stability in replant soils. Correlation analyses highlighted interactions between replant-sensitive soil fungi (Alternaria-group), the loss of soil structure and suppressed tree vigour, which become obvious only at specific time intervals. Full article
Show Figures

Figure 1

Article
Influence of Two Important Leguminous Trees on Their Soil Microbiomes and Nitrogen Cycle Activities in a Primary and Recovering Secondary Forest in the Northern Zone of Costa Rica
Soil Syst. 2020, 4(4), 65; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4040065 - 06 Nov 2020
Viewed by 862
Abstract
Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in [...] Read more.
Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in a primary and secondary forest were assessed for N-cycle metrics and DNA sequence-based composition of total bacterial, potential N-fixing bacterial, and potential ammonium oxidizing bacterial genera. The compositions of the functional groups of bacteria, but not their total relative abundance of DNA, were different across the soils. The P. macroloba soils had greater NO3 levels and richness of both functional groups, while I. edulis soils had greater NH4+ levels, consistent with its NH4+ preference for root nodule development. The bacterial communities were different by habitat, as secondary forest I. edulis microbiomes were less rich, more dominant, possibly more affected by the disturbance, or reached equilibrium status quicker than the richer, less dominant P. macroloba microbiomes, which may be developing slower along with secondary forest succession, or were less affected by the disturbance. Functional redundancy and switching of 10 N-cycle bacterial genera was evident between the primary and secondary forest soils, likely to maintain stable levels of N-cycle activity following disturbance. In summary, the two tree soil microbiomes are different, land use differentially affects them, and, thus, both tree species should be used during forest regeneration strategies in this region. Full article
Show Figures

Figure 1

Article
Short-Term Effects of Sewage Sludge Compost Amendment on Semiarid Soil
Soil Syst. 2020, 4(3), 48; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4030048 - 05 Aug 2020
Cited by 6 | Viewed by 1317
Abstract
The adoption of sewage sludge as an agricultural management strategy to improve soil properties and crop production is attracting great interest. Despite many positive effects on soil inorganic and organic components reported for different soil types, little information is available on sewage sludge [...] Read more.
The adoption of sewage sludge as an agricultural management strategy to improve soil properties and crop production is attracting great interest. Despite many positive effects on soil inorganic and organic components reported for different soil types, little information is available on sewage sludge application on Mediterranean soils, as well as on its use at different dose rates. The objectives of the present research was to evaluate, through an integrated approach, the effects of sewage sludge compost from urban wastewater on physicochemical, hydrological, biochemical parameters, and microbiota composition in soil pots under a three-year crop rotation system. Four different doses of sewage sludge compost (C3, C6, C9, C12) from municipal wastewater and a dose of them in combination with mineral fertilizer (C6N) were used. We have used 3-6-9-12 Mg/ha of sewage sludge compost for the treatments C3, C6, C9 and C12, respectively, and 6 Mg/ha of sewage sludge compost in combination with 60 kg/ha of ammonium nitrate for the treatment C6N.The effects were compared to non-fertilized (C0) and mineral fertilized (Min) sets of controls. The electrical conductivity, soil pH, stability of soil aggregates, percent of moisture of the dry soil both at the field capacity and at the wilting point, available P, and exchangeable K were all positively affected by increasing the amounts of composted sludge. The organic carbon and total N increased up to 66% and 39%, respectively. Increased enzymatic activities and microbial biomass were also observed in soil after the application of sewage sludge compost when compared to un-amended control. A higher richness and evenness among the soil plots amended with sewage sludge compost was observed, with no significant differences among the application dose rates, when compared to the un-amended soil control and soil treated with a mineral fertilizer. A three-year amendment was able to separate soil plots amended with high doses of sewage sludge compost from the low dose amended and control samples. Among the microbial groups responsible for such marked separation, bacteria belonging to Actinobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes contribute the most, with a shift from oligotrophic to copiotrophic taxa. Significant changes in bacterial composition and taxonomic structure should be considered in order to properly balance agronomic and economic advantages with environmental concerns. After all, our results have evidenced the effects of sewage sludge amendment on different soil properties, microbial activity, and composition already after a short period of application. The findings are particularly relevant in semiarid soils, where an immediate restoration of soil fertility by short-term compost application is needed. Full article
Show Figures

Figure 1

Article
Effect of Cathode Material and Its Size on the Abundance of Nitrogen Removal Functional Genes in Microcosms of Integrated Bioelectrochemical-Wetland Systems
Soil Syst. 2020, 4(3), 47; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4030047 - 03 Aug 2020
Cited by 1 | Viewed by 1442
Abstract
Constructed wetland-microbial electrochemical snorkel (CW-MES) systems, which are short-circuited microbial fuel cells (MFC), have emerged as a novel tool for wastewater management, although the system mechanisms are insufficiently studied in process-based or environmental contexts. Based on quantitative polymerase chain reaction assays, we assessed [...] Read more.
Constructed wetland-microbial electrochemical snorkel (CW-MES) systems, which are short-circuited microbial fuel cells (MFC), have emerged as a novel tool for wastewater management, although the system mechanisms are insufficiently studied in process-based or environmental contexts. Based on quantitative polymerase chain reaction assays, we assessed the prevalence of different nitrogen removal processes for treating nitrate-rich waters with varying cathode materials (stainless steel, graphite felt, and copper) and sizes in the CW-MES systems and correlated them to the changes of N2O emissions. The nitrate and nitrite removal efficiencies were in range of 40% to 75% and over 98%, respectively. In response to the electrochemical manipulation, the abundances of most of the nitrogen-transforming microbial groups decreased in general. Graphite felt cathodes supported nitrifiers, but nirK-type denitrifiers were inhibited. Anaerobic ammonium oxidation (ANAMMOX) bacteria were less abundant in the electrochemically manipulated treatments compared to the controls. ANAMMOX and denitrification are the main nitrogen reducers in CW-MES systems. The treatments with 1:1 graphite felt, copper, plastic, and stainless-steel cathodes showed higher N2O emissions. nirS- and nosZI-type denitrifiers are mainly responsible for producing and reducing N2O emissions, respectively. Hence, electrochemical manipulation supported dissimilatory nitrate reduction to ammonium (DNRA) microbes may play a crucial role in producing N2O in CW-MES systems. Full article
Show Figures

Figure 1

Article
Subsoil Microbial Diversity and Stability in Rotational Cotton Systems
Soil Syst. 2020, 4(3), 44; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4030044 - 25 Jul 2020
Cited by 2 | Viewed by 1464
Abstract
Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons [...] Read more.
Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton–maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini–Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen’s Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70–1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management. Full article
Show Figures

Graphical abstract

Article
Microbe Biomass in Relation to Organic Carbon and Clay in Soil
Soil Syst. 2020, 4(3), 41; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4030041 - 08 Jul 2020
Cited by 4 | Viewed by 1409
Abstract
Soil microbes are key to nutrient cycling and soil formation, yet the impact of soil properties on microbe biomass remains unclear. Using 240 soil cores of 0–15 cm depth, taken at random points across six cattle-grazed pastures on an undulating landscape, we evaluated [...] Read more.
Soil microbes are key to nutrient cycling and soil formation, yet the impact of soil properties on microbe biomass remains unclear. Using 240 soil cores of 0–15 cm depth, taken at random points across six cattle-grazed pastures on an undulating landscape, we evaluated the biomass of microbes in soil as affected by naturally occurring variation in soil organic carbon (SOC), clay content, and local topography. The study pastures varied in historic land-use for crops or forage seeding. SOC was found to be greater in topographically low areas. In contrast, clay content was not related to topography, and clay deposition possibly varies with glaciation legacy. Microbial biomass carbon (MBC) was correlated positively with SOC, increasing from 700 mg kg−1 MBC at 25 g kg−1 SOC to 2240 mg kg−1 MBC at 90 g kg−1 SOC. Most likely, SOC promotes MBC through the release of water-soluble organic carbon. However, the response of MBC to clay content was negative, decreasing from 1340 mg kg−1 MBC at 5% clay to 880 mg kg−1 MBC at 30% clay. Small voids in association with clay particles likely restrict the access of microbes to SOC. The relationship between SOC and MBC illustrates the important role of SOC for soil function, in terms of nutrient availability and development of soil structure via the contribution of microbes. Lastly, there was considerable spatial variability in MBC across the 65 ha site, highlighting the importance of land-use histories and gradients in environmental variables, to determine the biomass of microbes in soil. Full article
Show Figures

Figure 1

Article
The Change of pH Value and Octolasion cyaneum Savigny Earthworms’ Activity under Stubble Crops after Spring Triticale Continuous Cultivation
Soil Syst. 2020, 4(3), 39; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4030039 - 04 Jul 2020
Viewed by 990
Abstract
The changes of pH value followed by various agricultural practices are crucial for biotic components of soil, along with other environmental factors, like temperature and moisture content. In this paper, the earthworms population in triticale continuous cultivation was monitored. Their presence associated with [...] Read more.
The changes of pH value followed by various agricultural practices are crucial for biotic components of soil, along with other environmental factors, like temperature and moisture content. In this paper, the earthworms population in triticale continuous cultivation was monitored. Their presence associated with various agrotechnical methods (e.g., stubble crops maintained as mulch, mineral fertilization without pesticides) were assessed twice by the handsorting method, and their presence during the triticale vegetation season (occurrence of coprolites) were monitored too. The aim of the study was to analyse the distribution of earthworm populations in cereal continuous cultivation fields, and whether they prefer any of the stubble crop species (Sinapis alba L., Phacelia tanacetifolia Benth., Fagopyrum esculentum Moench.), which were sown after triticale harvest. The results reveal the most abundant earthworms occurence in the F. esculentum objects (43.1% of all sampled earthworms, which consists of 42% and 47.2% of all sampled matured and juveniles individuals, respectively), and species homogeneity (dominate Octolasion cyaneum Savigny, 1826). The changes of pH varied through the triticale vegetation season, but didn’t exhibit severe variation between sampling sites. Using earthworm services in cropping systems after having enticed them to the field through stubble crop has the potential to boost agricultural sustainability. Their ecological preferences, along with their trophic behaviour, have already been put in place to complete a case study of the autecology of the O. cyaneum Savigny 1826 species. Full article
Show Figures

Figure 1

Review

Jump to: Research

Review
Continuous Cropping Alters Multiple Biotic and Abiotic Indicators of Soil Health
Soil Syst. 2020, 4(4), 59; https://0-doi-org.brum.beds.ac.uk/10.3390/soilsystems4040059 - 23 Sep 2020
Cited by 14 | Viewed by 1932
Abstract
The continuous cropping (CC) of major agricultural, horticultural, and industrial crops is an established practice worldwide, though it has significant soil health-related concerns. However, a combined review of the effects of CC on soil health indicators, in particular omics ones, remains missing. The [...] Read more.
The continuous cropping (CC) of major agricultural, horticultural, and industrial crops is an established practice worldwide, though it has significant soil health-related concerns. However, a combined review of the effects of CC on soil health indicators, in particular omics ones, remains missing. The CC may negatively impact multiple biotic and abiotic indicators of soil health, fertility, and crop yield. It could potentially alter the soil biotic indicators, which include but are not limited to the composition, abundance, diversity, and functioning of soil micro- and macro-organisms, microbial networks, enzyme activities, and soil food web interactions. Moreover, it could also alter various soil abiotic (physicochemical) properties. For instance, it could increase the accumulation of toxic metabolites, salts, and acids, reduce soil aggregation and alter the composition of soil aggregate-size classes, decrease mineralization, soil organic matter, active carbon, and nutrient contents. All these alterations could accelerate soil degradation. Meanwhile, there is still a great need to develop quantitative ranges in soil health indicators to mechanistically predict the impact of CC on soil health and crop yield gaps. Following ecological principles, we strongly highlight the significance of inter-, mixture-, and rotation-cropping with cover crops to sustain soil health and agricultural production. Full article
Show Figures

Figure 1

Back to TopTop