Special Issue "Soil Quality and Ecosystem"

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A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (31 August 2012)

Special Issue Editors

Guest Editor
Prof Dr. Martin Romantschuk

Department of Environmental Sciences, University of Helsinki, Niemenkatu 73 C, FIN-15140, Lahti, Finnland
Website | E-Mail
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 | E-Mail
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

Special Issue Information

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

Published Papers (5 papers)

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Research

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Open AccessArticle 454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome
Diversity 2013, 5(1), 73-98; doi:10.3390/d5010073
Received: 20 January 2013 / Revised: 5 February 2013 / Accepted: 6 February 2013 / Published: 21 February 2013
Cited by 22 | PDF Full-text (1208 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving
[...] Read more.
Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils. Full article
(This article belongs to the Special Issue Soil Quality and Ecosystem)
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Open AccessArticle Aboveground Deadwood Deposition Supports Development of Soil Yeasts
Diversity 2012, 4(4), 453-474; doi:10.3390/d4040453
Received: 16 October 2012 / Revised: 27 November 2012 / Accepted: 4 December 2012 / Published: 10 December 2012
Cited by 10 | PDF Full-text (342 KB) | HTML Full-text | XML Full-text
Abstract
Unicellular saprobic fungi (yeasts) inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities,
[...] Read more.
Unicellular saprobic fungi (yeasts) inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities, soils collected underneath decaying wood logs and under forest litter were analyzed. We isolated and identified molecularly a total of 25 yeast species, including three new species. Occurrence and distribution of yeasts isolated from these soils provide new insights into ecology and niche specialization of several soil-borne species. Although abundance of typical soil yeast species varied among experimental plots, the analysis of species abundance and community composition revealed a strong influence of wood log deposition and leakage of organic carbon. Unlike soils underneath logs, yeast communities in adjacent areas harbored a considerable number of transient (phylloplane-related) yeasts reaching 30% of the total yeast quantity. We showed that distinguishing autochthonous community members and species transient in soils is essential to estimate appropriate effects of environmental factors on soil fungi. Furthermore, a better understanding of species niches is crucial for analyses of culture-independent data, and may hint to the discovery of unifying patterns of microbial species distribution. Full article
(This article belongs to the Special Issue Soil Quality and Ecosystem)
Figures

Open AccessArticle The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol
Diversity 2012, 4(4), 375-395; doi:10.3390/d4040375
Received: 29 August 2012 / Revised: 11 October 2012 / Accepted: 19 October 2012 / Published: 31 October 2012
Cited by 13 | PDF Full-text (729 KB) | HTML Full-text | XML Full-text
Abstract
Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in
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Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in a subtropical Acrisol was studied in south Brazil. The plots at this site represent two tillage systems, two nitrogen fertilization regimes and three crop rotation systems. Using Illumina high-throughput sequencing of the 16S rRNA gene, the archaeal and bacterial composition was determined from phylum to species level in the different plot treatments. The relative abundance of these taxes was correlated with measured soil properties. The P, Mg, total organic carbon, total N and mineral N were significantly higher in the no-tillage system. The microbial diversity was higher in the no-tillage system at order, family, genus and species level. In addition, overall microbial composition changed significantly between conventional tillage and no-tillage systems. Anaerobic bacteria, such as clostridia, dominate in no-tilled soil as well as anaerobic methanogenic archaea, which were detected only in the no-tillage system. Microbial diversity was higher in plots in which only cereals (oat and maize) were grown. Soil management influenced soil biodiversity on Acrisol by change of composition and abundance of individual species. Full article
(This article belongs to the Special Issue Soil Quality and Ecosystem)
Open AccessArticle Soil Nematodes and Their Prokaryotic Prey Along an Elevation Gradient in The Mojave Desert (Death Valley National Park, California, USA)
Diversity 2012, 4(4), 363-374; doi:10.3390/d4040363
Received: 27 August 2012 / Revised: 16 September 2012 / Accepted: 27 September 2012 / Published: 15 October 2012
Cited by 3 | PDF Full-text (526 KB) | HTML Full-text | XML Full-text
Abstract
We characterized soil communities in the Mojave Desert across an elevation gradient. Our goal was to test the hypothesis that as soil quality improved with increasing elevation (due to increased productivity), the diversity of soil prokaryotes and nematodes would also increase. Soil organic
[...] Read more.
We characterized soil communities in the Mojave Desert across an elevation gradient. Our goal was to test the hypothesis that as soil quality improved with increasing elevation (due to increased productivity), the diversity of soil prokaryotes and nematodes would also increase. Soil organic matter and soil moisture content increased with elevation as predicted. Soil salinity did not correlate to elevation, but was highest at a mid-gradient, alluvial site. Soil nematode density, community trophic structure, and diversity did not show patterns related to elevation. Similar results were obtained for diversity of bacteria and archaea. Relationships between soil properties, nematode communities, and prokaryotic diversity were site-specific. For example, at the lowest elevation site, nematode communities contained a high proportion of fungal-feeding species and diversity of bacteria was lowest. At a high-salinity site, nematode density was highest, and overall, nematode density showed an unexpected, positive correlation to salinity. At the highest elevation site, nematode density and species richness were attenuated, despite relatively high moisture and organic matter content for the soils. Our results support emerging evidence for the lack of a relationship between productivity and the diversity of soil nematodes and prokaryotes. Full article
(This article belongs to the Special Issue Soil Quality and Ecosystem)

Review

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Open AccessReview Enhancing Soil Quality and Plant Health Through Suppressive Organic Amendments
Diversity 2012, 4(4), 475-491; doi:10.3390/d4040475
Received: 26 November 2012 / Revised: 5 December 2012 / Accepted: 10 December 2012 / Published: 14 December 2012
Cited by 19 | PDF Full-text (276 KB) | HTML Full-text | XML Full-text
Abstract
The practice of adding organic amendments to crop soils is undergoing resurgence as an efficient way to restore soil organic matter content and to improve soil quality. The quantity and quality of the organic matter inputs affect soil physicochemical properties and soil microbiota,
[...] Read more.
The practice of adding organic amendments to crop soils is undergoing resurgence as an efficient way to restore soil organic matter content and to improve soil quality. The quantity and quality of the organic matter inputs affect soil physicochemical properties and soil microbiota, influencing different parameters such as microbial biomass and diversity, community structure and microbial activities or functions. The influence of organic amendments on soil quality has also effects on crop production and plant health. The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases. However, there is great variability in the effectiveness of suppression depending on the nature of the amendment, the crop, the pathogen, and the environmental conditions. Although the effects of organic amendments on soil properties have been widely studied, relationships between these properties and soil suppressiveness are not still well understood. Changes in soil physicochemical parameters may modulate the efficacy of suppression. However, the parameters more frequently associated to disease suppression appear to be related to soil microbiota, such as microbial biomass and activity, the abundance of specific microbial groups and some hydrolytic activities. This review focuses on the effect of organic amendments on soil microbial populations, diversity and activities; their ability to enhance plant health through disease suppression; and which of the parameters affected by the organic amendments are potentially involved in soil suppressiveness. Full article
(This article belongs to the Special Issue Soil Quality and Ecosystem)

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