Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes

Abstract

The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-016-0837-2) contains supplementary material, which is available to authorized users.

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

“…It has contributed to the emergence of metagenomics, i.e., an analysis of the genome of microorganisms by only DNA extraction without the necessity of cultivating microorganisms on artificial media [16,18,19]. Dijk et al [20] and Wolińska et al [21] suggested that the NGS technique contributed to overcoming the shortages and limitations that are connected with detection of only the most abundant and cultivated genera.…”

“…Another significant benefit of endophytes, which are important in the agricultural aspect, is their capability of nitrogen (N) fixation. The biological N fixation is a way of eliminating the use of chemical fertilizers and preventing damage to the agricultural ecosystem [21]. In the literature, there are some reports on N fixation by the legume plant-rhizobium system [52][53][54].…”

Actinobacteria Structure in Autogenic, Hydrogenic and Lithogenic Cultivated and Non-Cultivated Soils: A Culture-Independent Approach

“…Consequently, 16 samples for arable soils (coded C-as cultivated) and for non-cultivated sites (coded NC-as non-cultivated) were obtained. The scheme of soil sampling was presented in our previous study [18]. In laboratory conditions, each sample was air-dried and sieved through a 2-mm mesh.…”

“…All chemical parameters included in the current study were described and discussed in our previous studies [18,19,28]. The methods for determination of the moisture content, acidity (pH), and the concentrations of nitrogen biogenic forms (NH 4 -N, NO 3 -N, and NO 2 -N) were presented in Wolińska et al [18].…”

“…Thus, comprehensive knowledge of the structure and distribution of Actinobacteria in the soil environment is extremely desirable, as it can help to recognize positive or dangerous effects of the presence of Actinobacteria and, secondly, it can provide understanding of the impact of global environmental changes on the world's microbial communities [2]. Until recently, Actinobacteria have been mainly studied with conventional (culturing) methods [4][5][6]; however, Next Generation Sequencing -NGS techniques are currently applied for better recognition of the soil microbiota diversity [2,[15][16][17][18][19][20].…”