Biodiversity Of Soil Microorganisms Research Articles

Impacts of deforestation and forest regeneration on soil bacterial communities associated with phosphorus transformation processes in the Brazilian Amazon region

Land-use change has negative impacts on the biodiversity of plants and animals. However, we lack studies and/or information about the impacts of land-use change on the biodiversity of soil microorganisms, especially those involved in the phosphorus (P) transformation processes. This represents a great concern since some microbial groups are extremely important to different P transformation processes and regulate P availability in tropical and subtropical regions. In our study, we used shotgun DNA-metagenomic sequencing and P fractionation analysis to assess the effects of forest-to-pasture conversion on the dynamics of soil bacterial groups involved in the P transformation processes and their potential functions. Additionally, we assessed if the dynamics of these specific soil bacterial groups were recovered after pasture abandonment and with secondary forest establishment. Our results demonstrated that the land-use change altered the total amount of P and its fractions in the soils. The bacterial community structure was affected by changes in soil chemical properties, mainly by changes in the aluminum, total P, and labile P contents. The bacterial groups involved in the P transformation processes and their potential functions were also affected by changes in land use. The pasture soil harbored a distinct bacterial community when compared to the primary and secondary forest sites. In general, forest-to-pasture conversion increased bacterial groups involved in the P mineralization, including Firmicutes, Cyanobacteria, and Gemmatimonadetes. Conversely, we observed an increase of Proteobacteria members (e.g., Bradyrhizobiaceae and Beijerinckiaceae) and genes related to P solubilization and mineralization after pasture abandonment and with the secondary forest re-establishment. Our multi-analytical approach suggests that forest-to-pasture conversion has negative impacts on the biodiversity of bacterial groups involved in the P transformation processes and their potential functions, while the secondary forest re-establishment can stimulate resilience. Taken together, our results indicated that the bacterial groups involved in the P transformation and their potential functions can be gradually recovered and reach intermediate and/or even similar levels to those observed in undisturbed forest sites. This brings new insights and helps to improve our knowledge about the impacts of anthropogenic actions on the soil microbiome in the Amazon region.

Peatland degradation in Asia threatens the biodiversity of testate amoebae (Protozoa) with consequences for protozoic silicon cycling

Anthropogenic peatland degradation is a global threat. As peatlands store large amounts of carbon (C) their potential for mitigation of climate change has been emphasized recently. Global C cycling is linked to silicon (Si) fluxes from the continents into the oceans. These fluxes in turn are driven by biosilicification, the incorporation of inorganic Si into living organisms, in terrestrial ecosystems. Biosilicification by testate amoeba (TA) communities and its potential for Si cycling has been highlighted since the beginning of the 21st century. However, the effects of peatland degradation on TA biodiversity and corresponding protozoic biosilicification on a continental scale remained unresolved so far. We show that TA biodiversity in Asian peatlands is strongly affected by the grade of human impact. This biodiversity decline was accompanied by an unexpected increase in protozoic biosilicification. Our findings provide new insights into the interactions between the biodiversity of soil microorganisms and biogeochemical Si cycling.

Glyphosate-based herbicides alter soil carbon and phosphorus dynamics and microbial activity

Glyphosate is among the most used herbicides worldwide. However, both the active ingredient and additives of the commercial formulations may adversely affect chemical and biological processes in soil. Therefore, the aim of this work was to evaluate the effect of glyphosate and the commercial formulation (CH) on soil C, N and P dynamics, and microbial enzyme activity in two soil management conditions: a nopal plot (NP) with an history of 5 years of glyphosate application, and in an abandoned plot (AP) with a history of previous agricultural management without glyphosate applications. We performed three experiments: a) glyphosate and CH effects on phosphorus sorption by performing a non-biological P fixation experiment; b) glyphosate and CH effects on microbial activity, C, N and P dynamic, and the biodiversity of soil microorganisms in terms of biomarker fatty acids after a 27 day incubation experiment; and c) glyphosate and CH degradation was tested isolating bacteria from the incubated soil samples and growing in a defined media with potassium phosphate, glyphosate or CH as sole source of P. Our results suggested that other compounds from CH may be affecting P sorption, because when the herbicide was applied, P sorption was reduced in the NP, but in AP soil no significant effects were observed. In contrast, in the AP soil both glyphosate and the CH reduced C mineralization. Besides, CH application reduced Pmic concentration and laccase activity, but increased the specific activity of phosphonatase and phosphodiesterase in the AP soil. Additionally, the microbial community in NP soil revealed higher diversity index than the AP soil, but major changes in microbial groups were shown only when CH was applied. In vitro assay with native bacterial isolates confirmed their susceptibility to the commercial herbicide in both NP and AP soils. In conclusion, our results demonstrated changes on some processes related to soil C and P dynamics when pure glyphosate and a commercial glyphosate were applied, along with changes in microbial activity and community structure, being stronger the effects with the commercial formulation used. Further research should be done for test the effects of glyphosate on microbial stoichiometry and enzyme stoichiometry.

Is soil management system really important? comparison of microbial community diversity and structure in soils managed under organic and conventional regimes with some view on soil properties.

The fertility and productive value of soil are closely related to the physical and chemical properties of the soil as well as its biological activity. This activity is related to the intensity of microbially catalysed processes of transformation of organic and mineral substances contained in the soil. These processes are closely correlated with the abundance and biodiversity of soil microorganisms, especially bacteria, and the activity of enzymes produced by them. In this article we have compared some physicochemical properties of soil derived from conventional and organic farms and microbial communities inhabiting these ecosystems. We aim to investigate whether the soil management regime affects the abundance and diversity of these environments in terms of bacteria. Some differences in microbial communities were observed, but the rhizosphere of plants from organic and conventional soils does not harbour separate microbiomes. Albeit, the method of fertilization influences the diversity of soil microorganisms. A greater diversity of bacteria was observed in soils from farms where organic fertilizers were applied. Soil pH and activity of some soil enzymes were also shown to differ between organic and conventional soil cropping systems.

Effect of Mycorrhizal Inoculation and Irrigation on Biological Properties of Sweet Pepper Rhizosphere in Organic Field Cultivation

The aim of the study was to evaluate the influence of mycorrhizal fungi (MF) and irrigation on biological properties of sweet pepper rhizosphere in organic field cultivation. For this purpose, MF were applied to plants in the form of commercial mycorrhizal inoculum (Rhizophagus aggregatus, R. intraradices, Claroideoglomus etunicatum, Endogone mosseae, Funneliformis caledonium, and Gigaspora margarita) and irrigation according to the combinations: mycorrhized plants (PM), mycorrhized and irrigated plants (PMI), and irrigated plants (PI). Plants without MF and irrigation served as the absolute control (P). The study used classic and molecular techniques, assessing catalase activity, biodiversity of soil microorganisms (soil DNA analysis), and the Community-Level Physiological Profiles (CLPP) analysis using Biolog EcoPlates. The highest catalase activity was recorded in the control and mycorrhized soil sample. The highest total number of bacteria was noted in the rhizosphere of control plants (P) and irrigated plants, while the lowest number in the rhizosphere of mycorrhized and irrigated plants. Plant irrigation contributed to the increase in the total number of fungi in the rhizosphere. The rhizospheric soil of PM and PMI were characterized by the highest utilization of amines, amides, and amino acids, whereas the lowest level of utilization was detected in the P and PI rhizospheres. The highest biodiversity and metabolic activity were observed in the rhizospheres from the PMI and PM samples, whereas lower catabolic activity were recorded in the P and PI rhizospheres. The mycorrhization of crops improved the biological properties of the rhizosphere, especially under conditions of drought stress.

Biodiversity of Soil Microorganisms and their Effects on Disease Management at Black Pepper Farms in Gia Lai Province

Research on soil ecological systems, such as the soil characteristics and properties of the soil micro-flora system, is essential in the sustainable production of black pepper (Piper nigrum L.).The role of using beneficial microorganisms in the sustainable production of black pepper is in increase because many people are being aware of the hazards associated with consuming products with chemical substances. Twenty-seven soil samples were collected from Chu Se, Chu Prong and Duc Co district of Gia Lai province to determine the relationships between the ecological system, pathogenic fungi and nematodes in black pepper farms. The obtained results showed that the soil micro flora community was quite diverse. The average total density microorganism in Duc Co district, Chu Prong district and Chu Se district was of 8.41x106 CFU/g, 6.76x106 CFU/g and 8.91x106 CFU/g, respectively. The density of average total beneficial microorganisms in Duc Co district, Chu Prong district and Chu Se district was of 20.03x104 CFU/g, 14.25x104 CFU/g and 17.62x104 CFU/g, respectively. The use of organic fertilizers is common to the farms where high microbial densities were recorded. The relationship between the density of beneficial microorganisms (Nitrogen fixing bacteria, Phosphorus soluble bacteria, Cellulose degradation bacteria) and the density of fungal pathogens and nematodes was negatively correlated with R = - 0.84 and R = - 0.81 respectively. The results of correlation analysis showed that the density of beneficial microorganisms in the soil and the incidence of diseases in orchards were negatively correlated (R = - 0.69). This study proposes that the correlation between the basic factor of soil ecological system with pathogenic fungi and nematodes plays a very important role in biological control and the sustainable production of black pepper.

Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot.

SummarySoils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.

Insights on data collection for soil microbial diversity analyses

Soil bacterial communities have long been recognized as important ecosystem components, and have been the focus of many local and regional studies. However, there is a lack of data at large spatial scales, on the biodiversity of soil microorganisms; national or more extensive studies to date have typically consisted of low replication of haphazardly collected samples. This has led to large spatial gaps in soil microbial biodiversity data. Using a pre-existing dataset of bacterial community composition across a 16-km regular sampling grid in France, we show that the number of detected OTUs changes little under different sampling designs (grid, random, or representative), but increases with the number of samples collected. All common OTUs present in the full dataset were detected when analyzing just 4 % of the samples, yet the number of rare OTUs increased exponentially with sampling effort. We show that far more intensive sampling, across all global biomes, is required to detect the biodiversity of soil microorganisms. We propose avenues such as citizen science to ensure these large sample datasets can be more realistically achieved. Furthermore, we argue that taking advantage of pre-existing resources and programs, utilizing current technologies efficiently and considering the potential of future technologies will ensure better outcomes from large and extensive sample surveys. Overall, decreasing the spatial gaps in global soil microbial diversity data will increase our understanding on what governs the distribution of soil taxa, and how these distributions, and therefore their ecosystem contributions, will continue to change into the future.

MICROBIOME BIODIVERSITY OF SOYBEAN RHIZOSPHERE UNDER APPLICATION OF FUNGICIDES AND INOCULATION BY MICROBIAL BIOFORMULATION ECOVIT

Biodiversity of soil microorganisms in the agroecosystems plays the major role for stabilization and conservation of soil fertility, increasing plants productivity. Aim. To study the diversity of microbiome phylums of the dark-grey podzolic soil in the soybean rhizosphere, the seeds treated by fungicides with following inoculation with the complex microbial bioformulation Ecovital. Methods. Molecular-biological methods, pyrosequencing of PCR-amplicons of 16S rRNA gene V-4 region. Results. In soybean rhizosphere microbiome, there were identified 20 phylums, 28 classes and 44 orders of Bacteria, and one phylum, one class and two orders of Archaea. The representation of Proteobacteria phylum has increased from 26.2% in the control sample to 35.8–37.6% in the samples with the application of fungicides and inoculation, Bacteroidetes, Firmicutes and Acidobacteria phylums has increased from 1.5%, 2.1% and 11% in the control sample to 3.5–5.4%, 2.6–4.7% and 12.8–13.3% in all researched samples, respectively. The increase of biodiversity indices (Shannon’s and Menhinik’s indices) and the decrease of dominance indices (Simpson’s and Berger-Parker’s indices) indicate the increase of biodiversity for the samples with application of complex inoculant Ecovital and fungicides with Ecovital. Conclusions. Complex inoculation and its combined use with fungicides have promoted the increase of prokaryotes biodiversity in soybean rhizosphere.

Responses of microorganisms and enzymes to soil contamination with metazachlor

A greenhouse pot experiment was conducted at the University of Warmia and Mazury in Olsztyn, with the aim of describing the influence of metazachlor on counts and biodiversity of soil microorganisms, soil enzymatic activity, physicochemical properties of soil and yield of spring oilseed rape. The first experimental factor was soil contamination with increasing rates of metazachlor: 0 (soil without the herbicide), 0.333 (recommended by the manufacturer), 6.666, 13.332, 26.665, 53.328, 106.656 and 213.312 mg kg−1 dm of soil, while the second factor comprised two dates of determination: 30 and 60 days after starting the experiment. The tested herbicide had an adverse effect on reproduction of all analyzed microorganisms: oligotrophic bacteria and their endospore forms, Azotobacter spp. bacteria, organotrophic bacteria, actinomycetes and fungi. The values of the colony development and eco-physiological diversity indices decreased under the influence of excessive doses of the herbicide. Also, significant fluctuation in the enzymatic activity of soil was observed in response to the higher doses of metazachlor and depending on the date of determinations. The herbicide had an invariably negative influence on the activity of soil enzymes, causing the inhibition of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase and β-glucosidase. The physicochemical status of soil depended significantly on the degree of soil contamination with the herbicide, same as the yield of spring oilseed rape.

Isolation And Characterization Of Soil Microbes Of Shekhawati Region, Rajasthan

AbstractBacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey at the Mody institute of Technology and science, Lakshmangarh, Sikar we isolated two microbes from soils using a biochemical and molecular methods. The isolates were sequenced by 16S rDNA, and designated as Pseudomonas sp. RK05 (HQ009799) and Uncultured gamma proteobacterium clone RK 04 (HQ009800). Results confirmed the hazardous effects of pollution on the distribution and biodiversity of soil microorganisms where most of the native beneficial microorganisms were disappeared or non-cultured under these stressed conditions compared to the normal non-polluted soils in the same governorate which is certainly affecting soil fertility and productivity. Results also proved the efficiency of molecular characterization as precise and fast techniques for determining soil biodiversity compared to the traditional cultivation methods.

Molecular characterization of soil microorganisms: effect of industrial pollution on distribution and biodiversity

The present study aimed to investigate variations in the diversity of the indigenous bacterial and fungal populations in contaminated soil. Soil samples were collected from highly contaminated agricultural soil adjacent to an industrial drain in the Nile Delta named the “Defsho” drain, located at the city of Kafr El-Dawar, 20 km south of Alexandria (Longitude 30.12917 and Latitude 31.13972). PCR has become a popular tool for the retrieval of the natural environmental rRNA genes that represent native microbial species. Soil DNA was extracted and the 16S and 18S rRNA genes were amplified using polymerase chain reaction (PCR) and gene cloning. About 5,000 clones were obtained and genotyped using denaturing high performance liquid chromatography (DHPLC) to fingerprinting the biodiversity in the soil. Clones, which give different peaks with DHPLC, were then subjected to partial sequencing. Five prokaryotic and two eukaryotic out of 1,000 recombinant clones were randomly selected and further studied by DNA sequencing analysis. These clones were designated PT and ET for prokaryotes and eukaryotes, respectively. Results confirmed the hazardous effects of pollution on the distribution and biodiversity of soil microorganisms where most of the native beneficial microorganisms were disappeared or non-cultured under these stressed conditions compared to the normal non-polluted soils in the same governorate which is certainly affecting soil fertility and productivity. Five prokaryotic (PT) and two eukaryotic (ET) recombinant clones were randomly selected and further studied by DNA sequence analysis. DNA sequencing revealed that most of the identified bacteria are members of the class Proteobacteria; subdivision Gammaproteobacteria; order Enterobacteriales and family Enterobacteriaceae. Two PT clones (PT2 and PT4) were identified as Shigella flexneri 301-AF499895; members of PT1 and PT3 were related to Escherichia sp. and the uncultured bacterium S000009863 while PT5 was uncultured bacterium-S000331457 in addition to unclassified member of Desulfobacteriaceae, subdivision Deltaproteobacteria. ET1 was uncultured Trichocomaceae clone HC-B1/1-AF548306 and ET2 represents uncultured fungus clone SBS8w47f-AY681463, respectively. In conclusion, the significant decline in the genetic diversity in Defsho soil emphasized the hazardous effect of the industrial pollution on the biodiversity, stability and functioning of the native microbial population. Results also proved the efficiency of molecular characterization as precise and fast techniques for determining soil biodiversity compared to the traditional cultivation methods.