Functional Redundancy of Soil Microbiota – Does More Always Mean Better?

The proper and healthy functioning of the soil depends largely on the microorganisms abundance, including the total number of bacteria and fungi, but also their diversity. The increase in the biodiversity also increases the functional capabilities of the ecosystem but from a certain point, a further increase in the biodiversity does not bring any new features, so the general biochemical and metabolic profile of the ecosystem remains constant. It is also suggested that the loss of one or more species does not dramatically affect the functioning of the ecosystem, because the same functions can be represented by many different species. This phenomenon is called a functional redundancy and makes the soil a very stable environment with a high buffering capabilities, more often called the "soil memory". On the other hand, some unique biochemical processes are characteristic for a small group of species, for example, nitrogen fixation or toxic compounds degradation. The loss of the specialized species may lead to the decrease of a rare genes occurrence in the soil, resulting in the loss of nutrients or the accumulation of toxins. This article presents the current findings on functional redundancy in terms of soil microorganisms and its implications to the soil functioning

The Molecular‐Based Methods Used for Studying Bacterial Diversity in Soils Contaminated with PAHs (The Review)

Soil contamination could adversely affect microbial diversity, and perhaps also above‐ and below‐ground ecosystem functioning. It is important to study microbial diversity not only for basic scientific research, but also to understand the link between diversity and community structure and function in the pollution site. The study of microbial diversity and their function in contaminated soil creates a serious problem because they observed significant limitations in methodology and taxonomy of this group. Methodology for the determination of bacterial diversity does not include their function in the soil and other environment areas. Microbes are known for their catabolic activity in bioremediation, but changes in microbial communities are still unpredictable. The bioremediation of a pollutant and its rate depend on the environmental conditions, number and type of the microorganisms, nature and chemical structure of the chemical compound being degraded. However, molecular methods have been used to study soil bacterial communities. While many anthropogenic activities, such as city development, agriculture, and use of pollution, can potentially affect soil microbial diversity, it is unknown how changes in microbial diversity can influence below‐ground and above‐ground ecosystems. There are problems associated with studying bacterial diversity in soil. These arise not only from methodological limitations, but also from a lack of taxonomic knowledge. Methods to measure microbial diversity in soil can be categorized into two groups: biochemical‐based techniques and molecular‐based techniques. But more common for studying microbial diversity in soil contaminated with polycyclic aromatic hydrocarbons are the molecular methods

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment

The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5–21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles

Impact of AMF Claroideoglomus etunicatum on the structure of fungal communities in the tomato rhizosphere

Mycorrhizal fungi influence the development and activity of communities of soil microorganisms. The purpose of this study was to estimate the effect of arbuscular mycorrhizal fungus Claroideoglomus etunicatum (W. N. Becker & Gerd.) C. Walker & Schüβler on the population structure of fungal colonies in the rhizosphere of tomatoes grown in a plastic tunnel. The field experiment was conducted from 2015 to 2017 at an ecological farm in Grądy, central eastern Poland. The object of study were the three tomato cultivars: ‘Antalya F1’, ‘Esmira F1’, and ‘Pelikan F1’. Tomato seedlings were inoculated with C. etunicatum; spores were introduced about 5 cm deep in the rhizosphere of the studied plants (25–30 spores of C. etunicatum for each plant). Each year, mycological analysis of the tomato rhizosphere was conducted using Warcup’s method; structure of fungal communities of the tomato rhizosphere varied depending on the AMF applied. Saprotrophic fungi such as Trichoderma ssp., Mucor spp., and Penicillium spp. were often more isolated from the rhizosphere of plants inoculated with C. etunicatum than that of the control samples. It can be concluded that AMF directly impacted the development of fungal biodiversity in the tomato rhizosphere, particularly regarding the number of saprotrophs in the soil

Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons

Soil contamination with petroleum, especially in the area of oil wells, is a serious environmental problem. Restoring soil subjected to long-term pollution to its original state is very difficult. Under such conditions, unique bacterial communities develop in the soil that are adapted to the contaminated conditions. Analysis of the structure and function of these microorganisms can be a source of valuable information with regard to bioremediation. The aim of this study was to evaluate structural and functional diversity of the bacterial communities in soils with long-term impacts from petroleum. Samples were taken from the three oldest oil wells at the Crude Oil Mine site in Węglówka, Poland; the oldest was established in 1888. They were collected at 2 distances: (1) within a radius of 0.5 m from the oil wells, representing soil strongly contaminated with petroleum; and (2) 3 m from the oil wells as the controls. The samples were analyzed by 16S rRNA sequencing and the community level physiological profiling (CLPP) method in order to better understand both the genetic and functional structure of soil collected from under oil wells. Significant differences were found in the soil samples with regard to bacterial communities. The soils taken within 0.5 m of the oil wells were characterized by the highest biodiversity indexes. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria were strongly correlated with biological activity in these soils. Families of Alphaproteobacteria were also dominant, including: Bradyrhizobiaceae, Rhizobiaceae, Rhodobacteraceae, Acetobacteraceae, Hyphomicrobiaceae, and Sphingomonadaceae. The study showed that the long term contamination of soil changes bacterial communities and their metabolic activity. Even so, natural bioremediation leads to the formation of specific groups of bacteria that actively grow at the site of contamination in the soil

Fungal community change in selected fluvisols under simulated flooding condition

The soil mycobiome is an important part of the numerous biogeochemical processes taking place in the soil. Its activity and diversity are influenced by many factors, including soil moisture. In this study, the effect of a 14-day simulated flood on the mycobiome of three different Fluvisols in microcosm experiment was assessed using next-generation sequencing. The results obtained showed that excessive moisture alters the structure of the mycobiome and the amounts of pathogenic, parasitic, and endophytic fungi. Among others, an increase in the occurrence of saprotrophic fungi of the genera Trichoderma, Talaromyces, and Schizothecium was noted. At the same time, the study showeda decrease in the abundance of arbuscular mycorrhizal fungi from the phylum Glomeromycota and Mucoromycota as a result of flooding. In addition, the structure of the soil mycobiome has been shown to be closely related to soil type – statistically significant correlations of individual fungal genera with the clay and silt or sand content of the soil were obtained. Future research on the soil mycobiome under flooding conditions may help to understand changes in soil biogeochemical processes following flooding, the occurrence of which is increasing with climate change

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function

Fungal genetic biodiversity and metabolic activity as an indicator of potential biological weathering and soil formation – Case study of towards a better understanding of Earth system dynamics

Terrestrial plants act as ecosystem engineers modifying the flow of energy and matter and creating new habitats for other organisms. This vital concept also encompasses plants' effects on landforms and soils, crucial components of forested landscapes worldwide. In the present study, we investigate how trees through their roots and symbiotic organisms influence soil-weathering processes. The aim of the study was to answer one of the big questions in Earth sciences: how do biological agents, including fungi, acting at the critical interface between the biosphere and the abiotic environment, shape soil and landscape evolution? Within the present study we ask what is the level of fungal activity within root systems of trees and how can it influence biological weathering. The area of interest is in the Poprad River gorge in the southern part of the Sącz Beskidy Mountains, the Outer Western Carpathians. We applied the following analyses: 1) determination of the structural diversity of fungi (ITS1) and 2) assessment of the metabolic profile of soils (Biolog FFPlates). The highest average number of classified genera were fungi which simultaneously carried out pathotrophic, saprotrophic and symbiotrophic functions. Boletales, Agaricales, Cantharellales and Archaeorhizomycetales were the most abundant orders, but in one sample we also found a particularly high proportion of the order Mortierellales. The order Boletales and its family Boletaceae were significantly enriched in rock crack samples, whereas the highest number of differentially abundant taxa was observed in reference samples. The most frequently utilised substrates by fungi were: glycyl-L-glutamic acids, L-ornithine, L-phenylalanine, L-proline, D-galacturonic acid, fumaric acids, D-saccharic acids, succinic acids and N-acetyl-D-glucosamine. Our study demonstrates that the fungal community in the root zone is geochemically active and the organic acids secreted by plant roots in oligotrophic conditions and nutrient limitations significantly affect soil weathering

Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event

Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned

Community-Level Physiological Profiles of Microorganisms from Different Types of Soil That are Characteristic to Poland—a Long-Term Microplot Experiment

Comparative studies, such as the analysis of physicochemical properties and the microbiological composition of soil, are burdened with many problems resulting from the various locations of soils—often, different weather conditions among the experimental fields and varying time between the sample collection and analysis. The aim of this study was to assess the differences in the physiological profiles of bacterial communities from eight different types of soils from Poland, used in the microplot experiment that was established in 1881. The same plant species were continuously grown at all plots, at the same time, and the soil received the same type of fertilization. Moreover, the soils were always under the same weather conditions. The community-level physiological profiles of microorganisms were evaluated by using the Biolog EcoPlate™ method. The analysis demonstrated that good quality soils, especially the Gleyic Chernozem, Cambic Leptosol, and the Fluvic Cambisol exhibit a significantly higher enzyme activity, compared with the dystric soils. The dehydrogenases activity in the different time-points indicates a wide soil microbiome buffering capacity, which allows the persistence of a relatively permanent physiological profile, over many years