Special Issue "Soil Quality and Ecosystem"

Guest Editor
Prof Dr. Martin Romantschuk
Department of Environmental Sciences, University of Helsinki, Niemenkatu 73 C, FIN-15140, Lahti, Finnland
Website: https://tuhat.halvi.helsinki.fi/portal/en/organisations-researchgroups/martin-romantschuk-%284f2ed42b-05f1-4e87-8bb6-54d6a1ff8360%29.html
E-Mail: martin.romantschuk@helsinki.fi
Phone: +358 9 191 20334
Interests: environmental biotechnology; environmental molecular biology; bioremediation

Guest Editor
Dr. Janice E. Thies
Department of Crop and Soil Sciences, Cornell University, 722 Bradfield Hall, Ithaca, NY 14853, USA
Website: http://css.cals.cornell.edu/cals/css/people/faculty.cfm?netId=jet25
E-Mail: jet25@cornell.edu
Phone: +1 607 255 5099
Fax: +1 607 255 8615
Interests: soil ecology; biogeochemistry; soil microbiology; soil quality; biofertilizers; nitrogen fixation; agroecology; sustainable small-holder farming; international agriculture

Dear Colleagues,

The soil is a very versatile habitat for microbes, plant roots and soil-dwelling animals. The soil contains numerous microhabitats with widely differing conditions in locations even very close to each other, allowing for example, strict anaerobes to cohabitate with strict aerobes in even very small soil particles. Soil conditions change rapidly with changes in soil moisture, temperature and other variables; thus, an important trait for soil organisms is to be able to adapt and, when necessary, enter dormancy until conditions suitable for growth return. The adaptation to a life shifting between active growth and dormancy presents challenges for soil molecular ecology research in that it is difficult to distinguish between actively metabolizing cells, dormant cells, or the mere presence of dead cells still retaining their DNA. Novel methods are now available to try to meet this challenge.

Soil organisms live in close proximity and interact actively with each other. This is particularly true in the plant rhizosphere, where the plant roots, in symbiosis with mycorrhizal fungi support a much higher microbial density and probably also diversity than the bulk soil. Soil was one of the first environments for which it was shown that the true diversity is very much higher than what could be demonstrated by cultivation methods. The diversity seen with nucleic acid based methods is at least one to two orders of magnitude higher than what could be demonstrated by plating. The new sequencing techniques now in use shift the bottle neck from the generation of sequencing data to the handling of the raw sequence data and, in particular, to make biological and ecological sense out of it. An additional challenge is to determine the phylogenetic position of the “unknown” microbes, that is, fungi, bacteria, and archaea that have no close relatives among the cultivated, well characterized organisms.

Finally, a group of biological entities whose ecological role is only beginning to emerge are the viruses. Their ecological and evolutionary roles are being explored in the oceans, but study of viruses in soil has been slow, possibly due to practical difficulties. Much waits to be explored regarding microbial dynamics in soil, particularly activities that may be significantly influenced by viruses.
This special issue “Soil Quality and Ecosystem” focuses on the microbial diversity in different soil types, and on the interaction of microorganisms with plants and soil animals that create the ecosystems and the organismal dynamics of studied soils.

Prof Dr. Martin Romantschuk
Dr. Janice E. Thies
Guest Editor

Submission

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Type of Paper: Article
Title: The Use of Near-and Mid-Infrared Spectroscopy in Predicting Soil Ecosystem Function
Author: David Hagerberg
Affiliation: Department of Microbial Ecology, Ecology Building, University of Lund, SE-223 62 Lund, Sweden; E-Mail: David.Hagerberg@tyrens.se
Abstract: The use of Near-Infrared (NIR) and Mid-Infrared (MIR) spectroscopy in agriculture has been extensively developed during the last 40 years. The technique has been used for measuring the chemical composition of cereals, fruit and vegetables, meat, etc. Recently, the use of spectroscopy as a rapid field technique for the evaluation of soil quality (i. e. soil carbon and nitrogen levels) has attracted the attention. The use of NIR- and MIR-spectroscopy ranges from agricultural applications to estimation of carbon sequestration in assessing measures against climate change. Several studies have shown that NIR and MIR spectra can be correlated to microbial biomass as well as microbial biomarkers and composition of soil fauna, but the relation between spectra and the composition of the soil biological community remains unclear. Are the spectral pattern correlated directly with the abundance of soil organisms, or do they reflect the quality of soil organic matter which subsequently governs the composition of the soil ecosystem? The aim of this review is to summarize the current knowledge of the use of NIR and MIR spectroscopy for the study of soil ecosystems, and to try to identify causal relations between the spectra, quality of soil organic matter and abundance of soil organisms. The results have implications for assessment of soil function, for example when the effects of soil pollution on soil health are estimated.

Type of Paper: Article
Title: Drastic Change in the Soil Microbial Diversity and Composition in Constructed Soils after Coal Mining
Authors: Patricia Dorr de Quadros ^1,2, Andressa de Oliveira Silveira ², Kateryna Zhalnina ¹, Austin Davis-Richardson ¹, Jennifer Drew ¹, Flavio A. de O. Camargo ² and Eric Triplett ¹
Affiliations: ¹ Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
² Department of Soil Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil; E-Mail: patriciaquadros@ufl.edu
Abstract: The process of coal extraction usually results in contamination of soil layers with pyrite, which is oxidized forming acidic compounds, also environmental disturbances associated including soil compaction, erosion, dust, noise, water pollution, and impacts on local biodiversity. The goals of this work were to evaluate the changes on soil microbial diversity, abundance, and composition in the biggest mining coal of Latin America. Sites at different phases of recuperation (3, 4, 5, 6 and 19 years after coal extraction) were compared with undisturbed soils (native forest and grassland). The 16s rRNA gene of the samples was sequenced, soil features including chemical compounds, soil heavy metals content, microbial biomass and enzyme concentrations of the soils were examined. Within bacteria and archaeal domains, 24 phyla, 46 classes, 95 orders, 191 families, 525 genera and 2005 species were detected. Soil from recent reconstructed sites showed lower microbial diversity, microbial biomass, glycosidase and beta-glycosidase concentrations compared to non-disturbed sites. At phylum level, were detected 7-fold less OTUs in reconstructed soils than in forest or grassland soils, exhibiting a drastic decrease of microbial diversity after soil reconstruction. The most abundant genera in constructed soils were Thiobacillus, Novosphingobium, Sphingomonas, Desulforomonas, Geobacter and Pelomonas. Bradyrhizobium was the most abundant genus in forest site (6,37% of total reads), and Bacillus in the grassland site (4,79 % of total reads). Actinobacteria were positively correlated with copper concentration on soils. The microbial diversity in sites from 3 to 19 year old sites increases over time, but does not reach the original levels observed at the undisturbed sites. This indicates that the disorder caused by mining in the usual soil restoration processes cannot recover soil quality to that of undisturbed soil.
Keywords: soil quality; microbial ecology; microbial diversity; coal mining; constructed soils

Type of Paper: Article
Title: Aboveground Dead Wood Deposition Supports Development of Soil Yeasts
Authors: Andrey Yurkov ^1,2, Thorsten Wehde ¹, Tiemo Kahl ³ and Dominik Begerow ¹
Affiliations: ¹ Geobotany, Department of Evolution and Biodiversity of Plants, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
² Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
³ Institute of Silviculture, University of Freiburg, Tennenbacherstraße 4, 79085 Freiburg, Germany; E-Mail: a.yurkov@campus.fct.unl.pt
Abstract: The impact of aboveground dead wood deposition on soil yeasts was studied in three managed forests located in Swabian Alps, Germany. Yeast communities composition and structure was investigated in soils collected underneath decaying wood logs and in adjacent areas under forest litter. We isolated and identified molecularly a total of 25 yeasts including three new species. Unlike soils underneath wood logs, yeast communities in adjacent areas harbored considerable number of phylloplane-related yeasts reaching 30% of the total yeast quantity. This fact explains higher total yeast counts in soils under decaying wood. Overall, species composition of different localities was very heterogeneous and three to four species were common for soil communities underneath wood logs. However, the similarity between soil samples taken apart from wood logs was significantly lower. The analysis of species abundance and community composition revealed a strong influence of decaying wood logs. Cryptococcus podzolicus was the most frequent and abundant species underneath wood logs, but it was absent in soils collected in adjacent areas. Relative abundance of the most common yeast C. terricola was slightly higher in soils apart from wood logs, where it was dominant. Kazachstania piceae and Trichosporon porosum were more abundant in underneath wood logs and additionally displayed plot-specific pattern. Occurrence and distribution of yeasts isolated from soils provides a new insight into ecology and individual niche of several species. On average, decaying wood logs supported a more evenly structured yeast community suggesting also higher productivity of this habitat.
Keywords: yeasts; soil; wood decomposition; forest; Cryptococcus podzolicus