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Microorganisms
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Meta-Omics of Soil Microbiomes
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Meta-Omics of Soil Microbiomes

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 11548

Special Issue Editors

Dr. Stefano Ghignone

E-Mail Website
Guest Editor
National Research Council, Institute for Sustainable Plant Protection, 10125 Turin, Italy
Interests: plant symbiotic interactions; arbuscular mycorrhizal fungi; symbiosis; bioinformatics; soil microbiome; genomics; numerical ecology
Dr. Franco Magurno

E-Mail Website
Guest Editor
Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
Interests: mycorrhiza fungi; arbuscular mycorrhiza; mycorrhizal symbiosis; soil microorganism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, we have witnessed the astonishing scale and speed of the democratization of next-generation sequencing technologies (NGS), which have triggered an impressive contribution to the exploration of several aspects of microbial ecology.

Particularly soil environments, as the vault of the most diversity on the planet, have benefitted from the terrific resolution provided by NGS in disentangling communities and unveiling part of the microbial dark matter.

The detailed knowledge of microbiomes in soil is essential to address correct and effective conservation or recovery policies, whether these environments are natural, anthropized or subjected to high pressures of industrial exploitation.

In this Special Issue of Microorganisms, we invite you to submit both original research and review-type contributions regarding any aspect related to the use of -omics techniques in the study of soils, with particular focus on metagenomics, metagenetics, and metatranscriptomics approaches, used in the exploration of soil microbial community dynamics and their functional characterization.

Dr. Stefano Ghignone
Dr. Franco Magurno
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 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 microbial communities
  • Microbiome
  • Metagenomics
  • Amplicon Analysis
  • Metagenetics
  • Metatranscriptomics

Published Papers (3 papers)

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Research

12 pages, 2269 KiB  
Article
Influence of Manure Application on the Soil Bacterial Microbiome in Integrated Crop-Livestock Farms in Maryland
by Mengfei Peng, Zajeba Tabashsum, Patricia Millner, Salina Parveen and Debabrata Biswas
Microorganisms 2021, 9(12), 2586; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122586 - 15 Dec 2021
Cited by 5 | Viewed by 2802
Abstract
As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the production of animals and crops in a shared environment. The ICLFs in the mid-Atlantic region of the United States practice sustainable manure aging or composting processes to provide an on-farm source of [...] Read more.
As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the production of animals and crops in a shared environment. The ICLFs in the mid-Atlantic region of the United States practice sustainable manure aging or composting processes to provide an on-farm source of soil amendment for use as natural fertilizer and soil conditioner for crop production. However, crop fertilization by soil incorporation of aged manure or compost may introduce different microbes and alter the soil microbial community. The aim of this study was to characterize the influence of aged or composted manure application on the diversity of soil bacterial community in ICLFs. Soil samples from six ICLFs in Maryland were collected before (pre-crop) and during the season (2020–2021) and used to analyze soil bacterial microbiome by 16S rDNA sequencing. Results showed that both phylum- and genus-level alterations of soil bacterial communities were associated with amendment of aged or composted manure. Particularly, Proteobacteria and Actinobacteria were enriched, while Acidobacteria, Bacteroidetes, Planctomycetes, Firmicutes, and Chloroflexi were reduced after manure product application. Meanwhile, the relative abundance of Bacillus was decreased, while two zoonotic pathogens, Salmonella and Listeria, were enriched by manure amendments. Overall, animal manure amendment of soil increased the phylogenetic diversity, but reduced the richness and evenness of the soil bacterial communities. Although manure composting management in ICLFs benefits agricultural sustainable production, the amendments altered the soil bacterial communities and were associated with the finding of two major zoonotic bacterial pathogens, which raises the possibility of their potential transfer to fresh horticultural produce crops that may be produced on the manured soils and then subsequently consumed without cooking. Full article
(This article belongs to the Special Issue Meta-Omics of Soil Microbiomes)
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24 pages, 5066 KiB  
Article
The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire
by Sara Laetitia Elphège Gnangui, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Kadio Koua, Claude Ghislaine Zaka Kouadjo, Don A. Cowan and Adolphe Zézé
Microorganisms 2021, 9(9), 1842; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091842 - 30 Aug 2021
Cited by 6 | Viewed by 3112
Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil [...] Read more.
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making. Full article
(This article belongs to the Special Issue Meta-Omics of Soil Microbiomes)
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17 pages, 2973 KiB  
Article
Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria
by Anna Hegyi, Tran Bao Khuyen Nguyen and Katalin Posta
Microorganisms 2021, 9(9), 1796; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091796 - 24 Aug 2021
Cited by 18 | Viewed by 4066
Abstract
Bacterial communities can promote increased phosphorus (P) availability for plants and microbes in soil via various mechanisms of phosphate solubilization. The production of extracellular phosphatases releases available P through the hydrolysis of organic P. Examining the abundance and diversity of the bacterial community, [...] Read more.
Bacterial communities can promote increased phosphorus (P) availability for plants and microbes in soil via various mechanisms of phosphate solubilization. The production of extracellular phosphatases releases available P through the hydrolysis of organic P. Examining the abundance and diversity of the bacterial community, including phosphate solubilizing bacteria in soil, may provide valuable information to overcome P scarcity in soil ecosystems. Here, the diversity and relative abundance of bacterial phyla and genera of six agricultural soil samples from Vietnam were analysed by next generation sequencing of the 16S rRNA gene. Phosphatase activities of each soil were compared with physico-chemical parameters and the abundance of the alkaline phosphatase gene phoD. We showed the dominance of Chloroflexi, Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes. Total nitrogen positively correlated with phyla Proteobacteria, Acidobacteria, Firmicutes and Planctomycetes. The abundance of several genera of Proteobacteria showed positive relationship with the copy number of the phoD gene. The abundance of several taxa positively correlated with silt content, while a negative relationship of Proteobacteria was found with sand content. Our results demonstrated the clear influence of soil physico-chemical properties on the abundance of various bacterial taxa including those potentially involved in phosphate solubilization. Full article
(This article belongs to the Special Issue Meta-Omics of Soil Microbiomes)
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