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Diversity
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Genetic Diversity of Soil Bacterial Communities
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Genetic Diversity of Soil Bacterial Communities

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 20491

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. Carmine Crecchio

E-Mail Website
Guest Editor
Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
Interests: microbial ecology; soil microbial diversity; soil fertility; metagenomics of soil bacteria communities; plant-growth-promoting bacteria; biofertilizers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil is an important natural resource and has a key role in the biosphere, as most of the carbon and nutrient fluxes occur in the top 10 cm of the soil profile; it is a species-rich habitat that provides support for plant growth and health and, consequently, affects human activities. Although broadly homogeneous in the landscape, soil is extremely heterogeneous on a microbial scale. In fact, soil supports taxonomic and physiologic microbial diversity, which is regarded as more extensive than that of any other group of organisms and considered vitally important to the maintenance and sustainability of the biosphere.

Looking within the “black box”, as soil has been regarded in the last decades; overcoming its inaccessibility; and understanding its microbial composition and functioning, are challenges for scientists. In particular, if it is important to investigate the genetic diversity of microbial populations, it is also fundamental to understand the link between the major functions of microbial biomass and its species composition.

As Guest Editor for a Special Issue entitled "Genetic Diversity of Soil Bacterial Communities" to be published in the journal Diversity, I invite you to submit research articles, review articles, or short communications. Papers should address all the relevant and unclear aspects of the composition and functioning of bacterial communities, in agricultural and natural soil, in field trials, in laboratory-scale experiments, in rich or marginal soils, at different latitudes, and under different types of management.

Dr. Carmine Crecchio
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. Diversity 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 2600 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 bacterial diversity
  • Soil fertility
  • Metagenomics of soil bacteria communities

Published Papers (6 papers)

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Editorial

Jump to: Research, Review

2 pages, 150 KiB  
Editorial
Genetic Diversity of Soil Bacteria
by Carmine Crecchio
Diversity 2020, 12(11), 414; https://doi.org/10.3390/d12110414 - 29 Oct 2020
Cited by 1 | Viewed by 1690
Abstract
The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, [...] Read more.
The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)

Research

Jump to: Editorial, Review

20 pages, 4730 KiB  
Article
Impact of Various Grass Species on Soil Bacteriobiome
by Agata Borowik, Jadwiga Wyszkowska and Jan Kucharski
Diversity 2020, 12(6), 212; https://doi.org/10.3390/d12060212 - 26 May 2020
Cited by 11 | Viewed by 3122
Abstract
Today, various grass species are important not only in animal feeding but, increasingly often, also in energetics and, due to esthetic and cultural values, in landscape architecture. Therefore, it is essential to establish the roles various grass species and their functional forms play [...] Read more.
Today, various grass species are important not only in animal feeding but, increasingly often, also in energetics and, due to esthetic and cultural values, in landscape architecture. Therefore, it is essential to establish the roles various grass species and their functional forms play in modifying soil bacteriobiome and enzymatic activity. To this end, a pot experiment was conducted to examine effects of various fodder grass and lawn grass species on the bacteriobiome and biochemical properties of soil. Nonsown soil served as the control for data interpretation. Analyses were carried out with standard and metagenomic methods. The intensity of effects elicited by grasses depended on both their species and functional form. More favorable living conditions promoting the development of soil bacteria and, thereby, enzymatic activity were offered by fodder than by lawn grass species. Among the fodder grasses, the greatest bacteriobiome diversity was caused by sowing the soil with Phleum pratense (Pp), whereas among lawn grasses in the soil sown with Poa pratensis (Pr). Among the fodder grasses, the highest enzymatic activity was determined in the soil sown with Lolium x hybridum Hausskn (Lh), and among the lawn grasses—in the soil sown with Lolium perenne. Sowing the soil with grasses caused the succession of a population of bacterial communities from r strategy to k strategy. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
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20 pages, 4341 KiB  
Article
Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense
by Jadwiga Wyszkowska, Agata Borowik, Jacek Olszewski and Jan Kucharski
Diversity 2019, 11(12), 246; https://doi.org/10.3390/d11120246 - 17 Dec 2019
Cited by 21 | Viewed by 3315
Abstract
This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils [...] Read more.
This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
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11 pages, 1325 KiB  
Article
Nitrogen Fixing and Phosphate Mineralizing Bacterial Communities in Sweet Potato Rhizosphere Show a Genotype-Dependent Distribution
by Joana Montezano Marques, Jackeline Rossetti Mateus, Thais Freitas da Silva, Camila Rattes de Almeida Couto, Arie Fitzgerald Blank and Lucy Seldin
Diversity 2019, 11(12), 231; https://doi.org/10.3390/d11120231 - 03 Dec 2019
Cited by 10 | Viewed by 2906
Abstract
We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total [...] Read more.
We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total community DNA was extracted from the rhizosphere and analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), based on the alkaline phosphatase coding gene (alp gene) and on the nitrogenase coding gene (nifH gene). The cluster analysis based on DGGE showed that plant age slightly influenced the bacterial community related to phosphate mineralization in the rhizosphere of IPB-137, although it did not affect the bacterial community related to nitrogen fixation. The statistical analysis of DGGE fingerprints (Permutation test, p ≤ 0.05) showed that nitrogen-fixing bacterial community of IPB-052 statistically differed from genotypes IPB-149 and IPB-137 after six months of planting. The bacterial community of IPB-137 rhizosphere analyzed by alp gene also showed significant differences when compared to IPB-149 in both sampling times (p ≤ 0.05). In addition, alp gene copy numbers significantly increased in abundance in the rhizosphere of IPB-137 after six months of planting. Therefore, plant genotype should be considered in the biofertilization of sweet potato. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
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16 pages, 1018 KiB  
Article
Soil Biological Fertility and Bacterial Community Response to Land Use Intensity: A Case Study in the Mediterranean Area
by Mohammad Yaghoubi Khanghahi, Pasqua Murgese, Sabrina Strafella and Carmine Crecchio
Diversity 2019, 11(11), 211; https://doi.org/10.3390/d11110211 - 10 Nov 2019
Cited by 16 | Viewed by 3682
Abstract
The current study was performed to investigate the effects of three different long-term land use intensities on adjacent soil plots, namely a winter wheat field, a grass-covered vineyard, and a cherry farm, on soil biochemical, microbial, and molecular parameters. The results showed the [...] Read more.
The current study was performed to investigate the effects of three different long-term land use intensities on adjacent soil plots, namely a winter wheat field, a grass-covered vineyard, and a cherry farm, on soil biochemical, microbial, and molecular parameters. The results showed the maximum content of soil organic matter (SOM) and microbial biomass carbon (MBC) observed in the grass-covered vineyard. Basal respiration (BSR) and the cumulated respiration (CSR) after 25 days of incubation were significantly higher in the grass-covered vineyard and cherry farm, respectively (BSR 11.84 mg CO2–C kg−1 soil d−1, CSR 226.90 mg CO2–C kg−1 soil). Grass-covered vineyard showed the highest soil biological fertility index (BFI) score (20) and ranked in the class IV (good) of soil biological fertility. Cereal field and cherry farm had lower BFI scores and the corresponding BFI class was III (medium). In addition, the maximum ribosomal RNA copy number and the highest abundance of oligotrophic bacterial groups (25.52% Actinobacteria, 3.45% Firmicutes, and 1.38% Acidobacteria) were observed in the grass-covered vineyard. In conclusion, the grass-covered vineyard is a more conservative system and could have a large potential to improve total carbon storage in soil, mainly because of the cover crop residue management and the low soil perturbation through the no-tillage system. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
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Review

Jump to: Editorial, Research

16 pages, 346 KiB  
Review
Diversity of Rhizobia and Importance of Their Interactions with Legume Trees for Feasibility and Sustainability of the Tropical Agrosystems
by Emanoel G. Moura, Cristina S. Carvalho, Cassia P. C. Bucher, Juliana L. B. Souza, Alana C. F. Aguiar, Altamiro S. L. Ferraz Junior, Carlos A. Bucher and Katia P. Coelho
Diversity 2020, 12(5), 206; https://doi.org/10.3390/d12050206 - 24 May 2020
Cited by 9 | Viewed by 5119
Abstract
Symbiotic biological nitrogen fixation (BNF) is a complex process that involves rhizobia, a diverse group of α and β-proteobacteria bacteria, and legume species. Benefits provided by BNF associated with legume trees in tropical environments include improvements to efficiency of nitrogen (N) use, increase [...] Read more.
Symbiotic biological nitrogen fixation (BNF) is a complex process that involves rhizobia, a diverse group of α and β-proteobacteria bacteria, and legume species. Benefits provided by BNF associated with legume trees in tropical environments include improvements to efficiency of nitrogen (N) use, increase of soil carbon sequestration, stabilization of soil organic matter, decrease of soil penetration resistance, and improvement of soil fertility. All these benefits make BNF a crucial ecosystem service to the sustainability of tropical agriculture. Due to the importance of this ecological process and the high diversity of rhizobia, these bacteria have been extensively characterized worldwide. Currently, over 400 species of rhizobia are known, distributed into seven families. In the humid tropics, Leucaena leucocephala, Acacia mangium, Gliricidia sepium, and Clitoria fairchildiana are four of the most common species used by family farmers to create sustainable agricultural systems. These four legumes perform symbiosis with different groups of rhizobia. Exploring BNF could help to enable sustainable intensification of agriculture in the humid tropics, mainly because it can increase N use efficiency in an environment where N is a limiting factor to plant growth. Full article
(This article belongs to the Special Issue Genetic Diversity of Soil Bacterial Communities)
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